Table 1.

CRTRs

Genome coordinatesa
Windows <1% thresholdb
Total SNPsc
SNP class A/B/Cd
Monomorphic AD/ED/XDe
Rec ratef
Known genesg
CRTRs in the AD population
chr1: 41080000-41470000 29/30 137 106/27/4 26+/10-/19 1.2 CTPS, FLJ23878, SCMH1
chr2: 95300000-95940000 45/55 70 36/28/6+ 4/13/10 0.1 TRIM43, AK024144 TRIM51, OR5W2, OR10AG1, AK055955, OR5F1, OR5AS1, OR8I2, OR8H2, OR8H3, OR8J3, OR8K5, OR5J2, OR5T2, OR5T3
chr11: 55340000-55750000 32/32 431 390/39/2- 42/37-/279+ 0.0 OR5T1, FLJ43276, ZSCAN2, SCAND2, FLJ14888
chr15: 82780000-83180000 24/31 —h —h —h 0.0 NMB, SPC18, ZNF592
chr16: 14460000-14760000 21/21 39 35/4/0 11+/5/34+ 1.8 PARN, BFAR, PLA2G10
chr20: 20360000-20720000j 27/27 164 133/31/0 11/63+/81+ 2.4 AB033098
chr22: 26700000-27190000 35/40 267 259/7/1- 31+/91+/115+ 2.4 PITPNB, KIAA1043, SFPQ, ZNF262, PKD1L, NCDN, TFAP2E, PSMB2
CRTRs in the ED population
chr1: 35220000-36210000 87/90 192 155/29/8 13/84+/41 0.9 CLSPN, EIF2C4, EIF2C1, EIF2C3
chr2: 84470000-84810000 25/25 192 101/88/3+ 22/83+/75+ 0.2 SUCLG1, FLJ37357
chr2: 162820000-163240000 25/33 228 221/5/2- 75+/88+/72 0.4 GCG, FAP, IFIH1, GCA, KCNH7
chr3: 89690000-90110000 33/33 110 47/61/2+ 3/31/32 0.1 i
chr4: 32930000-33560000 50/54 276 215/50/11 17/92+/141+ 0.6 i
chr4: 148880000-149280000 31/31 200 176/18/6- 11/85+/85+ 0.8 TMEM34, ARHGAP10
chr6: 75060000-75360000 21/21 139 116/23/0 16/34/23 0.0 i
chr6: 75580000-75890000 22/22 142 70/69/3+ 29+/37/48 0.0 i
chr6: 84500000-84800000 21/21 118 96/22/0 7/31/50+ 0.2 NCB50R
chr6: 105600000-105980000 22/29 166 119/37/10 2/40/59 0.8 BVES, POPDC3, PREP, AK025690, ARPC1A, ARPC1B, PDAP1, G10, PTCD1, CPSF4, ATP5J2, ZNF394, ZFP95, VIK
chr7: 98460000-99080000 52/53 135 76/51/8+ 7/54+/53 1.0 ZNF498, CYP3A5, CYP3A7, CYP3A4, VCIP135, FLJ11267, PTTG3, SGKL, FLJ25692
chr8: 67650000-68280000 47/54 93 67/15/11 15+/43+/89+ 0.4 COPS5, FLJ22490
chr10: 68630000-68930000 16/21 122 103/15/4 30+/36/27 0.7 CTNNA3, P4HA1, NUDT13, HSGT1, DNAJC9, MRPS16
chr10: 74340000-75090000 63/66 177 136/38/3 14/46/32 0.0 TTC18, ANXA7, ZMYND17, PPP3CB, USP54
chr11: 37980000-38360000k 29/29 281 201/78/2+ 12/91+/102 0.1 i
chr12: 42710000-43010000 20/21 174 162/9/3- 24+/55+/66 0.6 DKFZp434K2435
chr12: 87490000-87840000 26/26 124 98/24/2 9/46+/61+ 0.4 i
chr14: 44280000-44700000 33/33 177 142/29/6 15/39/58 0.6 BTBD5, KIAA0423, PRPF39
chr16: 46030000-46340000k 17/22 68 56/8/4 10/13/17 0.3 PHKB
chr18: 28630000-29170000 40/45 307 232/73/2 7/86+/101 0.6 C18orf34
chr18: 65710000-66040000k 24/24 247 228/17/2- 11/39/214+ 1.8 CD226, RTTN
chr19: 47540000-47920000 28/29 67 49/17/1 3/16/37+ 0.5 LIPE, CEACAM1, CEACAM8
chr20: 20360000-20690000j 21/24 151 124/27/0 11/62+/79+ 2.4 AB033098
CRTRs in the XD population
chr1: 72310000-72790000 39/39 358 317/38/3- 26/184+/217+ 0.2 NEGR1
chr1: 87010000-87320000 18/22 103 83/18/2 14/9/39 0.9 SEP15, HS2ST1
chr1: 92220000-93030000 68/72 252 150/96/6+ 20/37/79 0.6 BTBD8, GLMN, FLJ13150, GFI1, EVI5
chr1: 103130000-103460000 24/24 201 145/56/0+ 12/52/90+ 0.3 COL11A1
chr2: 84540000-84910000 28/28 197 133/59/5+ 17/90+/65 0.2 SUCLG1, FLJ37357, DNAH6, AB051484, SULT1C2, GCC2, LIMS1, RANBP2, FLJ32745
chr2: 108350000-109120000 68/68 360 309/37/14- 17/79/195+ 0.9 EDAR
chr2: 177390000-177730000 20/25 447 439/8/0- 24/125+/353+ 1.2 i
chr2: 189140000-189570000 31/34 245 204/41/0 17/85+/124+ 0.3 GULP1, DIRC1
chr2: 194650000-194990000 24/25 102 15/87/0+ 4/88+/37 0.2 i
chr3: 17570000-17890000 21/23 115 81/31/3 17+/18/69+ 0.6 TBC1D5
chr3: 25700000-26250000 46/46 229 154/70/5+ 10/72+/107+ 1.2 NGLY1
chr4: 41670000-42050000 29/29 181 150/29/2 2/20/59 1.2 TMEM33, SLC30A9, FLJ43695
chr5: 117360000-117700000 25/25 227 161/64/2+ 4/34/63 0.9 i
chr6: 126650000-127130000 39/39 110 79/31/0 6/30/37 0.8 i
EPHB6, TRPV6, TRPV5, KEL, OR9A2, OR6V1
chr7: 142030000-142360000 24/24 211 44/162/5+ 7/91+/103+ 0.3 C7orf34
chr8: 50580000-51170000 45/50 432 364/65/3 13/162+/193+ 0.4 SNTG1
chr11: 37820000-38290000k 38/38 377 295/80/2 13/108+/144+ 0.4 i
chr12: 22370000-22700000 24/24 134 124/8/2- 18/53+/49 0.9 KIAA0528
chr12: 86840000-87360000 41/43 147 88/44/15+ 6/23/43 0.5 FLJ35821, AL137488, Cep290, SMILE
chr13: 19040000-19390000 26/26 119 102/12/5 7/32/37 0.8 HSMPP8, PSPC1, ZNF237
chr13: 62440000-62760000 23/23 210 157/53/0 16/26/47 0.0 i
chr14: 67310000-67770000 36/37 257 229/25/3- 5/70+/159+ 0.3 RAD51L1
chr15: 61550000-62070000 43/43 262 233/26/3- 10/42/195+ 0.6 USP3, FBXL22, HERC1, DAPK2, BC058863, BCL7C, CTF1, FBXL19, HSD3B7
chr16: 30700000-31070000 26/28 48 12/34/2+ 2/20+/27+ 0.4 STX1B2, STX4A, FLJ13479, KIAA0296, VKORC1
chr16: 45180000-45500000 23/23 58 22/31/5+ 2/32+/37+ 0.0 VPS35, ORC6L, LOC91807, LOC388272
chr16: 46050000-46490000k 28/35 105 87/14/4 9/16/24 0.3 PHKB, CBFB, Lin10, TRADD, FBXL8, HSF4, NOL, E2F4, ELMO3, LRRC29, HSPC171, FHOD1, SLC9A5
chr16: 65590000-66060000 36/38 106 85/7/14 7/36+/51+ 0.3 AK097481, FLJ11004, CGI-38, ZDHHC1
chr17: 61300000-61640000 25/25 187 140/46/1 2/12-/30 1.4 AK096929
chr18: 28640000-29150000k
35/42
300
228/70/2
7/83+/98
0.6
C18orf34

a Genome coordinates in the hg17 build.

b Fraction of 100-kb windows <1% empiric threshold.

c Total number of Perlegen SNPs in the window.

d Perlegen class SNP counts. 106/27/4 indicates 106 class A, 27 class B, and 4 class C. + indicates significant excess of B relative to genome average, — indicates significant deficit of B relative to genome average.

e Count of monomorphic SNPs in each population. + indicates significant excess of monomorphic SNPs relative to genome average in a given population, — indicates significant deficit of monomorphic SNPs.

f Recombination rate for flanking megabase from deCODE sex averaged map.

g Known genes within CRTR derived from the UCSC Genome Browser Known Genes (November 22, 2004) track. Bold are resequenced genes.

h Not mapped in hg16.

i No known gene within CRTR.

j CRTR shared between ED and AD populations.

k CRTRs shared between ED and XD populations.