Return to Haplogroup R
Haplogroup R Private SNPs, Notes and Papers - 2014
SNP SYMBOLS:
Private
Investigation
|
NOTE: Corrections/Additions made to this page are shown at the bottom of the main Haplogroup R page.
Frequently Mutating SNPs are SNPs that appear many times in many places either in one or more
haplogroups. They are inconsistent and not useful for genealogical purposes.
- L128/PF3499 - listed 13 May 2014.
- L147 - Listed 14 May 2014.
R1a Private SNPs - After having been investigated, these SNPs have not met the population distribution
criteria for placement on the tree. Either too few confirmed positive testers have been found OR multiple
confirmed testers were confined to either a single surname or to a small group of related males.
- M56, M64.2/Page44.2, M87, M157.1, M204, M434, P98 and
PK5 are downstream of M417. Listed 19 July 2012.
- M334 is downstream of M458. Listed 19 July 2012.
- L175/S467 is downstream of L176.1/S179.1. Listed 19 July 2012.
- BY185.2/SUR33.2, BY186.2/SUR34.2, BY187.2/SUR35.2, BY189.2/SUR41.2,
BY190.2/SUR42.2, BY191.2/SUR43.2, BY192.2/SUR44.2, BY193.2/SUR45.2 are located at approximately Z2123. Listed
15 November 2014.
R1a SNPs under Investigation - Additional testing is needed to confirm adequate positive samples
and/or correct placement on the tree.
- L12, L235, L399, L450, L451, L458, L579
and Page68 are located at approximately R-M417. Listed 24 Jun 2011.
- L291 is located at approximately R-M458. Listed 24 Jun 2011.
- L457/PF6191 is located at approximately R-M417. Listed 19 July 2012.
- Z1222 and Z1223 are downstream of R-Z93. Listed
11 February 2012.
- F1493.3/M6377.3 is located downstream from CTS4179 and disjoint from L176.1. Listed
5 December 2013.
- SUR1, SUR2 are located at approximately Z2123. Listed 7 November 2014.
- KMS2 is located downstream from Z2123. Listed 7 November 2014.
R1b Private SNPs - After having been investigated, these SNPs have not met the population distribution
criteria for placement on the tree. Either too few confirmed positive testers have been found OR multiple
confirmed testers were confined to either a single surname or to a small group of related males.
- L5 is located downstream of R-U106. Listed 6 Apr 2006.
- S50 is located at approximately R-M269. Listed 6 Apr 2006.
- L50/S136 is located at approximately R-L23.
Listed 28 Oct 2010.
- L179 and L180
are located downstream of Z6. L179 and L180 were found in a single individual, and are likely phylogenetically
equivalent. Listed 21 Mar 2011.
- L3/S216 is located at approximately R-L562. Listed 10 Jul 2011.
- L135, L209 and S42 are
located at approximately R-L2. Listed 21 Mar 2011.
- L7, L95, L171, L173
and L194 are located at approximately R-P312. Listed 21 Mar 2011.
- L141.2 and S44 are located at approximately R-U152.
Listed 6 Aug 2011.
- L626 is located under L627. Listed 6 Aug 2011.
- L625 is located under R-L626. Listed 6 Aug 2011.
- M65 is located downstream of R-P312/S116. The position of private SNP
M65 is uncertain with respect to the positions of Z196, L238/S182, DF19 and DF27.
Listed 26 June 2012.
- M126 and M160 are located downstream R-S28/U152.
The positions of M126 and M160 are uncertain with respect to
the positions of L2, Z36, and Z56. Listed 26 June 2012.
- M228.2 is located downstream of R-L21/M529/S145. Listed 26 June 2012.
- M37 is located downstream of R-L21/M529/S145. The position of private SNP M37 is uncertain with respect to the positions
DF23/S193, DF1/L513, L96, L159.2/S169.2, Z253, DF21/S192, L371, and DF41. Listed 26 June 2012.
- L319.1 is located under R-DF13. Listed 8 July 2012.
- L302/S464 is located under R-DF49. Listed 8 July 2012.
- L9, L10 are located under
R-L513. Listed 8 July 2012.
- L894 and L895 are located downstream of R-L1066.
Listed 8 July 2012.
- L696 is downstream of Z326. Listed 18 July 2012.
- L653 is downstream of Z18. Listed 18 July 2012.
- L217.2/S1849.2 is downstream of Z7. Listed 18 July 2012.
- P107 is downstream from U106. Listed 9 August 2012.
- L6 is is downstream from U106. Listed 9 August 2012.
- L325 is downstream from Z18. Listed 9 August 2012.
- L188 is downstream from Z326. Listed 9 August 2012.
- V8 is downstream from V88 and parallel to M18. Listed 9 August 2012.
- V7 is downstream from V35. Listed 9 August 2012.
- L127.2 is located downstream from L128. Listed 18 August 2012.
- L259/S266 is located downstream from Z301. Listed 18 August 2012.
- M157.2 is located downstream from Z6. Listed 18 August 2012.
- L693 is located downstream from L48. Listed 19 August 2012.
- S420 is located downstream from S425; associated with Wilson surname.
Listed 13 September 2012.
- S3068 is located downstream of S302, S303, S421, and S422, but is above S420;
associated with Wilson surname. Listed 23 February 2014.
- S303, S421 are downtream from S425; associated with Wilson surname.
S421 occured after S422+S302. S303 occurred after S421. Listed 23 February 2014.
- FGC3251 is located downstream from FGC3221; associated with McClure surname.
Listed 13 November 2014.
- FGC20562 is located downstream from FGC20560 and parallel to FGC20561. Listed 17
November 2014.
- FGC20563 is located downstream from L1308. Listed 17 November 2014.
R1b SNPs under Investigation - Additional testing is needed to confirm adequate positive samples
and/or correct placement on the tree.
- L100 is located at approximately R-S47. Listed 21 Mar 2011.
- L216 is located at approximately R-L23. Listed 22 Mar 2011.
- L86.2, L220.1, L221, L253, L289, L326
and M228.1 are located at approximately R-P312. Listed 6 Aug 2011.
- L192.1 is located at approximately R-L21. Listed 26 June 2012.
- L408, L409, L199.3/L443.3/L675.3/PF5371.3, L552, L553 and L594 are
located at approximately R-L2. Listed 6 Aug 2011.
- L654.1 is located at approximately R-U152.
Listed 6 Aug 2011.
- L276, L628 and L659 are located downstream of R-M167.
Listed 6 Aug 2011.
- L629 is located at approximately R-Z196. Listed 6 Aug 2011.
- L641 and L642 are located at approximately R-DF21/S192.
Listed 6 Aug 2011.
- L671 is located at approximately R-Z36. Listed 4 Sep 2011.
- L132.2! is located downstream of R-L1. Listed 22 Dec 2011.
- L343 and L356 are located at approximately R-U152. Listed
26 June 2012.
- S372/Z258 and S492/Z384 are located at approximately R-Z367.
Listed 26 June 2012.
- Z276 is located at approximately R-Z34. Listed 26 June 2012.
- L737, L738, L739, Z383 and S256/Z291 are located at
approximately R-L20/S144. Listed 26 June 2012
- S245/Z245 is approximately equivalent to R-L21/M529/S145, L459. Listed 26 June 2012.
- S450/Z268 is approximately equivalent to Z209. Listed 8 July 2012.
- L1231 is located at approximately R-DF27. Listed 8 July 2012.
- L526, L564, L580 and L583 are located at approximately R-DF13.
Listed 8 July 2012.
- L577, L908 and L909 are located at approximately
R-L513. Listed 8 July 2012.
- L557/S394 and L561 are located at approximately R-L555.
Listed 8 July 2012.
- S261/YSC0000052/Z16 is approximate with Z18. Listed 18 July 2012.
- S500/Z153, Z154 and Z155 are downstream of Z301. Listed
18 July 2012.
- L782 is downstream of Z156. Listed 18 July 2012.
- L292 is downstream of L45. Listed 18 July 2012.
- S269/Z328, S1731/Z327, S1746/Z332, S1747/Z333, Z335 and
Z336 are approximate with Z326. Listed 18 July 2012.
- S381/Z81, S506/Z82, Z80 and Z83 are downstream of
Z326. Listed 18 July 2012.
- S473/Z261 is located downstream of L21. Listed 9 August 2012.
- S471/Z252 is located at approximately L21. Listed 9 August 2012.
- S359/Z229 is expected to be at the same node as F1343/S225/Z225. Both Z225 and Z229 were initially observed in
two Peruvian samples. Listed 17 August 2012.
- S302, S422 are downtream from S425. Listed 13 September 2012.
- S883/Z2184 is located at approximately Z2185 and is downstream of Z253 and upstream of L1066 and Z2183.
Listed 8 November 2012.
- Z2183 is located at approximately L1066 and is downstream of Z2184 and Z2185. Listed 8 November 2012.
- L1334 is located downstream of R-L1335/S530, parallel to L743. Listed 8 January 2013.
- L1358 is located downstream of R-U152. Listed 14 January 2013.
- L1245/S1264 and L1246/S1285 are located at approximately DF27.
Listed 10 March 2013.
- CTS6519/S4247, CTS11567/Z2572, DF79, DF81, DF83, DF84, S453/Z224, Z222 and
S360/Z223 are located under DF27. Listed 10 March 2013.
- Z260 is located at approximately L21. Listed 19 March 2013.
- Z2245 and Z2247 are located at approximately
L238. Listed 19 March 2013.
- S369/Z51 is located at approximately L562. Listed 19 March 2013.
- S653/Z2955, Z2962, Z2963, Z2964, S637/Z2970, S640/Z2972, S641/Z2973 and
S651/Z2988 are located at approximately M222. Listed 19 March 2013.
- CTS4716 is located at approximately or upstream of SRY2627. Listed 19 March
2013.
- L876 is located at approximately P314.2. Listed 19 March 2013.
- S234/Z199, S362/Z200, S457/Z201, Z202, Z203, Z204, Z264, Z266 and
Z269 are located at approximately SRY2627. Listed 19 March 2013.
- CTS7768/S1307 is located under Z195 and Z196, mutually exclusive with
Z209, Z220, and L176.2, and is approximately equivalent to DF17. Listed 19 March 2013.
- S357/Z215 is located at approximately Z209. Listed 19 March 2013.
- Z279 and Z299 are located at approximately Z214.
Listed 19 March 2013.
- CTS12074/S8070, PF7595/S358/Z211, PF7598/Z270, Z210, Z212, Z273 are located at
approximately Z216. Listed 19 March 2013.
- CTS11440 is located downstream from CTS2501. Listed 19 March 2013.
- L1312, PF3434.1 and
L1315 is located downstream from DF13. Found in a WTY with L1314.
Listed 19 March 2013.
- L1314 is located downstream from DF13. Found in a WTY with L1315.
Listed 19 March 2013.
- CTS5714/S1137, CTS8358 are located downstream from DF13. May be phylogenetically equivalent to
CTS4466. Listed 19 March 2013.
- Z3001 is located downstream from DF21.
Listed 19 March 2013.
- L247.2/S293.2 is located downstream from DF41. Listed 19 March 2013.
- CTS1202.2/L1066.2, F1237.2/M1077.2/V2083.2 and L1293 are located
downstream from L2. Listed 19 March 2013.
- CTS11795.2, PF121.2 are located downstream from L20. Listed 19 March 2013.
- L1333 is located downstream from L513. Listed 19 March 2013.
- S1468/Z57 is located downstream from L562. Listed 19 March 2013.
- S257/Z150 is located downstream from Z142. Listed 20 March 2013.
- CTS8002.2/PF2155.2, F3952.2, PF1169.2, PF1217 and
M3268.2/PF3292.2 are located downstream from M222. Listed 20 March 2013.
- CTS4299, CTS8289, PF742.2, S251/Z207, Z205 and
S362/Z208 are located downstream from M167/SRY2627. Listed 20 March 2013.
- CTS7193.2, F1493.2/M6377.2 and
PF4363 are located downstream from U152. Listed 20 March 2013.
- CTS1595, CTS5531/PF6636 and
CTS8492 are located downstream from Z143. Listed 20 March 2013.
- CTS9952 and
F3867.2 are located downstream from Z225. Listed 20 March 2013.
- F4036.2 and
PF1557.2 are located downstream from Z253. Listed 20 March 2013.
- CTS188, CTS4333 and
CTS7958 are located downstream from Z36. Listed 20 March 2013.
- Z259 is located downstream from Z367. Listed 20 March 2013.
- CTS9044 is located downstream from Z367 and may be be phylogenetically equivalent
to CTS8479.2/M5251.2/PF1746.2. Listed 20 March 2013.
- CTS8479.2/M5251.2/PF1746.2 is located downstream from Z367 and may be be phylogenetically equivalent
to CTS9044. Listed 20 March 2013.
- S259/Z46, S484/Z48, Z47 and S482/Z71are located downstream from Z56.
Listed 20 March 2013.
- L1200 is approximately equivalent to L1199. Listed 17 July 2013.
- CTS12966/DF87 is downstream of DF19 at approximately Z302. Listed 18 August 2013.
- DF93/S1687, DF94 is downstream of U198. Listed 18 August 2013.
- DF97 is downstream of DF85. Listed 18 August 2013.
- CTS3394, CTS5282, CTS5519, CTS7306, CTS8748, CTS9738 and CTS9805 are
located under R-Z253 and are believed to be mutually exclusive with L554, PF825.2, and Z2534. Listed 2 September 2013.
- S7402/Z12222 are downstream of Z142, approximate with Z150, unknown relationship with L562.
Listed 5 December 2013.
- S3106 is located equivalent to S423, however its stability is uncertain as Chromo2 data
indicates possible back-mutations at several different levels below S423. Listed 23 February 2014.
- F1265.2/M1313.2, S588/FGC4108, S659/DF105, S660/DF109, S661/DF104,
S7073/FGC462, S7814 are downstream of M222. Listed 7 March 2014.
- FGC3268 is located approximately downstream of Z253 and upstream of FGC3222. Listed
14 November 2014.
- FGC5507, FGC5508, FGC5510, FGC5511, FGC5512, FGC5513, FGC5521, FGC5522, FGC5523, FGC5524, FGC5530,
FGC5533, FGC5534, FGC5537, FGC5538, FGC5539, FGC5541, FGC5543, FGC5544, FGC5551, FGC5552, FGC5554, FGC5557,
FGC5558, FGC7448 are located at approximately DF13. Listed 14 November 2014.
- A40/FGC5583, A41/FGC8002, A43/FGC5594, A44, A47/FGC5605, A48/FGC5612, A98/FGC8622,
A99/FGC8624, A105/FGC8638, A106/FGC8643, A107/FGC8646, A108/FGC8647, A109/FGC8648, A110/FGC8649, A111/FGC8652,
A112/FGC8655, A113/FGC8659 are located at approximately CTS2501. Listed 14 November 2014.
- A118, A119, A120, A121, A127, A128, A129, A130, A131, A132, A133, A135, A136, A137, A138,
A139, A142, A144 are located at approximately FGC5496. Listed 14 November 2014.
- A89, A150/FGC11144, A151, A152, A153, A154, A155.2/Z12652.2, A159, A195/Z16253,
A664, A714, A726, A745, A806 are located at approximately CTS4466. Listed 14 November 2014.
- A228, BY246, BY247, BY248, BY249 are located at approximately L21.
Listed 14 November 2014.
- L150.2/PF6274.2/S351.2 is located downstream of M269. Listed 15 November 2014.
- FGC496/Z6749, FGC5561, S2202 are located downstream of FGC5494. Listed 15
November 2014.
- A19/S847, A287, A288/BY1, BY279 are located at approximately Z253. Listed 15
November 2014.
- A162, A163, A164, A165, A166, A167, A169, A170, A171, A172/ZS3079, A173.2/Z15291.2, A176,
A179, A180, A183, A185, A186.1/ZS2136.1, A187, A188.2/Z13583.2, A189, A191, A193, A194 are located at approximately
S2202 and downstream of FGC5494. Listed 15 November 2014.
- A223, A225, A259, A738/BY198, BY179/F1400, BY185.1/SUR33.1, BY186.1/SUR34.1,
BY187.1/SUR35.1, BY188, BY189.1/SUR41.1, BY190.1/SUR42.1, BY191.1/SUR43.1, BY192.1/SUR44.1, BY193.1/SUR45.1,
BY194 are located at approximately M222. Listed 15 November 2014.
- A226, A227, A317, A318, A319, A410, A411, A412, A415, A680 are located at
approximately L1/S26. Listed 16 November 2014.
- A241, A247 are located at approximately S470/Z251. Listed 16 November 2014.
- A260 is located at approximately S660/DF109. Listed 16 November 2014.
- A3 is located at approximately L193.1/S176.1. Listed 16 November 2014.
- A2/BY15/FGC13493, A4, A5, A6, A7/FGC13499, A8, A9, BY16/Z16361, BY17/FGC11802/Z16385,
BY180/Z18078, BY182/Z18079, BY183/Z18080, BY184/Z18081, BY206, BY207/Z18067, BY208/FGC21247 are located at
approximately DF1/L513/S215. Listed 16 November 2014.
- A430, A476, A479, A557, A558, BY239 are located at approximately S219/Z255.
Listed 16 November 2014.
- BY127, BY264 are located at approximately DF27/S250. Listed 16 November 2014.
- A433 is located at approximately P312/PF6547/S116. Listed 16 November 2014.
- A459 is located at approximately L1402. Listed 16 November 2014.
- A625/FGC19610 is located at approximately CTS6889/S116. Listed 16 November 2014.
- A96/FGC10292/Y2999 is located at approximately S276/Z6. Listed 16 November 2014.
- BY115/FGC14676, BY116/FGC14683, BY160/Z18014, BY161/Z18015, BY163/Z18017, BY164/Z18018,
BY165/Z18019, BY166/Z18021, BY167/Z18022, BY168/Z18023, BY169/Z18024, BY170/Z18025, BY171/Z18029,
BY172.2/SK563.2/Z17470.2, BY173/Z18030, BY174/Z18031, BY176/Z18035, BY177/Z18036, BY178/Z18037, BY280,
BY281, BY282, BY283, BY284, BY285, BY286, BY287, BY288, BY289, BY290, BY291, BY292, BY293, BY294, BY295, BY296,
BY297 are located at approximately CTS2501. Listed 16 November 2014.
- BY122, BY124 are located at approximately CTS7080/S3334. Listed 16 November 2014.
- BY129, BY131, BY132, BY133, BY134, BY135, BY209, BY210 are located at approximately
L165/S68. Listed 16 November 2014.
- A661/BY141, A662/BY142, BY140/Z17987, BY149/Z17981 are located at approximately
CTS4466/S1136. Listed 17 November 2014.
- BY143/S27835, BY144/FGC17829/S27834, BY150, BY153, BY154 are located at
approximately L1335/S530. Listed 17 November 2014.
- BY155 is located at approximately S756. Listed 17 November 2014.
- BY250, BY251 are located at approximately CTS9219. Listed 17 November 2014.
- A46/FGC5598 is located downstream of CTS2501. Listed 17 November 2014.
R2 SNPs under Investigation - Additional testing is needed to confirm adequate positive samples
and/or correct placement on the tree.
- L261, L288, L381, M367.2 and
M368.2 are located at approximately R2-M124. Listed 17 Mar 2011.
- L384 and L385 are located under R2-L294. Listed 17 Mar 2011.
- F820/Page4 is located at approximately R2-M479. Listed 17 Mar 2011.
- L722 and L726 are located at approximately R2-M124.
Listed 18 July 2012.
NOTES:
- Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in
the order of discovery, and separated by "/". Examples: M207/UTY2, M306/S1, M173/P241, SRY1532.2/SRY10831.2,
L23/S141, L48/S162, L11/S127, P310/S129, P311/S128, M405/S21/U106, M467/S29/U198, DYS439/L1/S26, P312/S116,
M167/SRY2627, S28/U152, L2/S139, L20/S144, L21/S145, M222/USP9Y+3636.
- The position of L196 is undertain with respect to the position of Z49
- L405/L584 (ChrY:27141305) is a triallelic SNP with allele values "A", "C", and "T". A value of "A" indicates haplogroup Y(xP)
and is referred to as L405-. A value of "C" indicates haplogroup P and is referred to as L405+ and a value of "T" indicates
haplogroup R1b1a2a1c and is referred to as L584+.
- L342.2 is known to co-mutate with L319.4, L348.3 and
L349.2 in haplogroup R1a; all should be derived if any one of them is.
Listed 7 Aug 2011.
- Due to lack of positive control samples for M56, M157.1, M64.2, M87, M204, P98, PK5, and M434, the positions of those
private or uncommon SNPs in the haplotree are uncertain with respect to the positions of Z93, Z280, and L176.1/S179.1.
- P25 is an unreliable SNP with a 2% reversion rate within R1b1. It should not be used by
itself to classify individuals. For further details see Adams et al (2006) and
Discussion of P25
- L49 is a recurrent mutation in Haplogroup R and may be generally unstable in Haplogroup R. In haplogroup
R1b1a2a, L49.1 is phylogenetically equivalent to L23. In haplogroup R1a1a1, L49.2 is located under M417.
In haplogroup R2a, L49.3 is located at or near P267.
- SNP SRY1532/SRY10831 appears twice on the Y-DNA Haplogroup tree. It is first seen as a mutation
SRY1532.1/SRY10831.1 which is reported as a positive in BT and then reappears as a back mutation
SRY1532.2/SRY10831.2 which is reported as a negative in R1a.
- Thomas Krahn has developed a new primer for DYS439-Null (aka L1, S26) that gives a score of 12 rather than null.
- Thanks to Jim Wilson and Thomas Krahn for their consultation on Haplogroup R.
- Data from the 1000 Genomes Project suggests that Z220 is downstream from Z209 and Z278 is downstream of Z216.
Listed 26 June 2012.
- The stability of S3028 is uncertain. Listed 23 February 2013.
- L195/S354, L144/S175 are STR mutations that happen back and forth so have been removed from the tree. Listed
26 November 2014.
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The Case of the Unreliable SNP: Recurrent Back-mutation of Y-chromosomal Marker P25 Through
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Strong Intra- and Inter-continental Differentiation Revealed by Y chromosome SNPs M269, U106 and U152.
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Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny.
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Herrera et al,
Neolithic Patrilineal Signals Indicate that the Armenian Plateau was Repopulated by Agriculturalists.
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New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup
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