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Table 1 SNP Frequencies and Hardy-Weinberg P-Values

From: The BRCA1 Ashkenazi founder mutations occur on common haplotypes and are not highly correlated with anonymous single nucleotide polymorphisms likely to be used in genome-wide case-control association studies

        Ashkenazi Jews (n = 85) CEPH (n = 60) African Americans (n = 48) Chinese Americans (n = 48) Mexican Americans (n = 48)
rs number SNP Number SNP name Position b33a Position b36.1b Com Allelec Min Alleled mafe P-value maf P-value maf P-value maf P-value maf P-value
13119 1 C_9270420 41373486 38718247 c t 0.424 0.580 0.350 0.712 0.177 0.624 0.396 0.359 0.458 0.961
748620 2 C_9270421 41373037 38717798 c g 0.440 0.640 0.350 0.712 0.240 0.550 0.391 0.518 0.465 0.669
17599948 3 C_9270454 41364175 38708936 a g 0.211 0.649 0.192 0.865 0.104 0.022 0.094 0.326 0.362 0.591
11653231 4 C_95201 41240225 38584986 g a 0.435 0.703 0.350 0.712 0.240 0.550 0.396 0.359 0.467 0.905
9908805 5 C_3178692 41230675 38575436 c t    0.008 0.948 0.375 0.878    0.011 0.941
2175957 6 C_11631183 41195587 38540348 t g 0.447 0.665 0.350 0.712 0.250 0.441 0.396 0.359 0.446 0.935
3092986 7 BR1_000340 41186761 38531522 a g 0.051 0.636 0.042 0.736 0.010 0.942    0.031 0.823
8176072 8 BR1_000392 41186709 38531470 t a 0.006 f 0.957         
8176074 9 BR1_000571 41186530 38531291 g a      0.010 0.942     
3765640 10 C_2615164 41185012 38529773 a g 0.440 0.640 0.350 0.712 0.228 0.740 0.394 0.433 0.444 0.592
NAg 11 M_185delAG 41184811 38529572 a - 0.006 0.957         
8176090 12 BR1_007918 41179183 38523944 c g    0.008 0.948 0.096 0.338     
1800062 13 BR1_010574 41176528 38521289 g a        0.021 0.883   
8176101 14 BR1_010796 41176306 38521067 a t      0.021 0.882     
8176103 15 C_2615171 41175815 38520576 g a 0.463 0.291 0.350 0.712 0.234 0.640 0.396 0.359 0.458 0.961
8176104 16 BR1_011340 41175762 38520523 g a 0.024 0.824 0.033 0.789      0.010 0.942
8176109 17 C_2615172 41174541 38519302 a g 0.441 0.497 0.350 0.712 0.239 0.609 0.396 0.359 0.469 0.751
8065872 18 BR1_016775 41170328 38515089 t a      0.135 0.278    0.010 0.942
8176120 19 BR1_017105 41169998 38514759 g a 0.424 0.913 0.350 0.712 0.240 0.550 0.396 0.359 0.458 0.961
799914 20 BR1_018573 41168546 38513307 g a      0.135 0.278     
799913 21 BR1_019408 41167711 38512472 a g 0.032 0.772 0.042 0.736 0.365 0.813    0.010 0.942
8176128 22 BR1_019904 41167215 38511976 t a      0.063 0.644     
8176133 23 BR1_020896 41166223 38510984 t g 0.422 0.738 0.350 0.712 0.167 0.488 0.396 0.359 0.458 0.961
799912 24 C_2615180 41165899 38510660 c t 0.472 0.701 0.364 0.926 0.125 0.322 0.396 0.359 0.489 0.882
799923 25 BR1_026422 41160696 38505457 c t 0.232 0.031 0.308 0.858 0.042 0.763    0.104 0.459
8176145 26 BR1_029258 41157859 38502620 t c 0.400 0.038 0.319 0.586 0.240 0.550 0.404 0.309 0.448 0.829
8176146 27 BR1_029448 41157669 38502430 c t 0.031 0.774 0.008 0.948       
7503154 28 BR1_030748 41156369 38501130 t g 0.415 0.618 0.339 0.478 0.223 0.771 0.396 0.359 0.468 0.862
1799950 29 BR1_031875 41155246 38500007 a g 0.077 0.442 0.042 0.736 0.010 0.942    0.031 0.823
4986850 30 BR1_032885 41154236 38498997 g a 0.133 0.096 0.113 0.071 0.033 0.819    0.013 0.935
16940 31 BR1_033119 41154002 38498763 t c 0.422 0.429 0.350 0.712 0.177 0.624 0.396 0.359 0.448 0.829
799917 32 BR1_033420 41153701 38498462 c t 0.429 0.766 0.358 0.868 0.125 0.322 0.396 0.359 0.479 0.571
4986852 33 BR1_003927 41153194 38497955 g a 0.012 0.912 0.042 0.736 0.010 0.942     
2227945 34 BR1_034226 41152895 38497656 a g      0.052 0.703    0.010 0.942
16942 35 BR1_034356 41152765 38497526 a g 0.433 0.868 0.348 0.615 0.245 0.521 0.396 0.359 0.447 0.716
799916 36 C_7530109 41151955 38496716 t g 0.438 0.482 0.358 0.868 0.271 0.703 0.394 0.433 0.479 0.894
2070833 37 BR1_035507 41151614 38496375 c a 0.031 0.001      0.271 0.726 0.135 0.167
2070834 38 BR1_036077 41151050 38495811 a c 0.435 0.626 0.342 0.568 0.250 1.000 0.396 0.359 0.438 0.634
8176158 39 BR1_036793 41150334 38495095 a g 0.418 0.393 0.353 0.665 0.174 0.532 0.396 0.359 0.458 0.961
8176160 40 BR1_036859 41150268 38495029 a g 0.435 0.626 0.350 0.712 0.240 0.550 0.396 0.359 0.458 0.961
8176166 41 BR1_038085 41149042 38493803 a g 0.196 0.391 0.150 0.172 0.104 0.022 0.120 0.632 0.344 0.395
8176174 42 BR1_040350 41146777 38491538 a t      0.063 0.644     
3950989 43 C_3178696 41146718 38491479 g a 0.441 0.566 0.348 0.615 0.234 0.640 0.396 0.359 0.457 0.923
8176175 44 BR1_040669 41146458 38491220 t - 0.006 0.956      0.073 0.586   
8176177 45 BR1_041288 41145840 38490601 a g      0.021 0.883     
8176178 46 BR1_041721 41145407 38490168 a g      0.042 0.763     
1060915 47 C_3178676 41143235 38487996 a g 0.380 0.105 0.352 0.851 0.177 0.624 0.396 0.359 0.468 0.862
3737559 48 C_3178677 41143069 38487830 c t 0.124 0.481 0.067 0.580    0.083 0.208 0.043 0.761
8176187 49 BR1_045154 41141974 38486735 t c          0.010 0.942
8176188 50 BR1_045505 41141623 38486384 t g      0.063 0.644     
6416927 51 BR1_0046019 41141109 38485870 g c        0.083 0.208   
8176198 52 BR1_047826 41139302 38484063 t a 0.422 0.429 0.362 0.427 0.348 0.114 0.426 0.761 0.479 0.571
8176199 53 BR1_0477839 41139289 38484050 a c 0.341 0.594 0.258 0.502 0.135 0.167 0.177 0.624 0.396 0.135
4239147 54 BR1_048551 41138577 38483338 t c 0.440 0.640 0.324 0.677 0.271 0.703 0.394 0.433 0.452 0.711
8176206 55 BR1_050244 41136885 38481646 a g      0.052 0.703    0.010 0.942
2236762 56 C_11621042 41135440 38480201 a t 0.435 0.626 0.358 0.868 0.271 0.703 0.406 0.581 0.479 0.894
1799966 57 C_2615208 41131859 38476620 t c 0.456 0.456 0.350 0.712 0.233 0.781 0.396 0.359 0.469 0.751
3092987 58 BR1_055669 41131488 38476249 a g 0.416 0.545 0.350 0.712 0.170 0.510 0.396 0.359 0.458 0.961
8176225 59 BR1_056796 41130361 38475122 g t      0.031 0.823     
8176232 60 BR1_058369 41128788 38473549 c t 0.013 0.936         
8176234 61 BR1_058614 41128545 38473306 a g 0.437 0.345 0.350 0.712 0.239 0.609 0.396 0.359 0.458 0.961
8176235 62 BR1_058834 41128325 38473086 g a 0.339 0.872 0.258 0.502 0.167 0.488 0.396 0.359 0.436 0.972
8176236 63 BR1_059589 41127570 38472331 t c    0.008 0.948 0.359 0.556    0.010 0.942
8176240 64 BR1_060022 41127137 38471898 t c      0.063 0.644     
8176242 65 BR1_060520 41126639 38471400 g a 0.433 0.538 0.350 0.712 0.170 0.510 0.406 0.581 0.458 0.961
8176245 66 BR1_061014 41126145 38470906 t c      0.063 0.644     
3092994 67 C_2615220 41124590 38469351 c t 0.434 0.471 0.350 0.712 0.228 0.242 0.396 0.359 0.266 0.808
8176259 68 BR1_062588 41124571 38469332 t -      0.052 0.703     
8176265 69 BR1_0064398 41122761 38467522 g a 0.417 0.477 0.350 0.712 0.167 0.729 0.394 0.433 0.260 0.848
2187603 70 BR1_064501 41122658 38467419 g a 0.422 0.429 0.350 0.712 0.167 0.729 0.396 0.359 0.260 0.848
8176273 71 BR1_066741 41120418 38465179 t c 0.424 0.580 0.342 0.568 0.167 0.729 0.396 0.359 0.260 0.848
8176278 72 BR1_067978 41119181 38463942 a g    0.008 0.948 0.500 0.564    0.021 0.883
8066171 73 BR1_068063 41119096 38463857 g t      0.146 0.237    0.010 0.942
NA 74 M_5382insC 41117845 38462606 - c 0.006 0.957         
8176289 75 C_2615230 41114821 38459582 t c 0.441 0.566 0.342 0.568 0.223 0.258 0.396 0.359 0.266 0.808
8176293 76 BR1_073023 41114136 38458897 a -        0.031 0.823   
4793192 77 BR1_074008 41113155 38457916 a g 0.435 0.626 0.336 0.794 0.229 0.214 0.396 0.359 0.260 0.848
8176296 78 BR1_074807 41112356 38457117 a g 0.435 0.703 0.350 0.712 0.229 0.214 0.396 0.359 0.260 0.848
3092988 79 C_2615238 41110467 38455228 c t 0.424 0.580 0.350 0.712 0.170 0.709 0.396 0.359 0.260 0.848
8176303 80 BR1_076933 41110230 38454991 a g      0.010 0.942 0.042 0.763   
8176305 81 BR1_077034 41110129 38454890 a g 0.094 0.753 0.092 0.442 0.021 0.883    0.010 0.942
8176307 82 BR1_077328 41109835 38454596 t c      0.063 0.644     
8068463 83 BR1_079220 41107943 38452704 c t      0.125 0.322     
8176313 84 BR1_079396 41107767 38452528 g a 0.006 0.957 0.017 0.896       
8176316 85 BR1_080570 41106594 38451355 c a      0.021 0.883     
8176318 86 BR1_081125 41106039 38450800 g t 0.435 0.963 0.350 0.712 0.167 0.729 0.385 0.491 0.250 1.000
12516 87 BR1_081990 41105173 38449934 c t 0.435 0.626 0.350 0.712 0.229 0.214 0.406 0.581 0.260 0.848
8176320 88 BR1_082035 41105128 38449889 g a 0.006 0.957 0.033 0.789      0.010 0.942
8176321 89 BR1_082199 41104964 38449725 g a      0.010 0.942     
8176323 90 BR1_082687 41104476 38449237 c g 0.429 0.766 0.350 0.712 0.229 0.214 0.396 0.359 0.260 0.848
7223952 91 C_11621012 41103649 38448411 t c 0.441 0.566 0.356 0.765 0.281 0.569 0.396 0.359 0.287 0.931
9911630 92 C_3178665 41097108 38441868 a g 0.422 0.429 0.364 0.926 0.266 0.808 0.396 0.359 0.283 0.813
11460963 93 C_2615245 41090062 38435121 - g 0.441 0.497 0.350 0.712 0.228 0.242 0.396 0.359 0.266 0.808
2298861 94 C_3178699 41085596 38430357 g a 0.441 0.309 0.350 0.712 0.223 0.258 0.396 0.359 0.266 0.808
2298862 95 C_3178698 41085453 38430214 t c 0.447 0.383 0.350 0.712 0.208 0.343 0.396 0.359 0.260 0.848
443759 96 C_2287905 41074499 38419260 c t 0.229 0.129 0.241 0.656 0.354 0.520 0.083 0.208 0.146 0.981
11871636 97 C_11617231 41063582 38408343 a c 0.235 0.304 0.259 0.386 0.302 0.345 0.167 0.083 0.135 0.278
2271539 98 C_1588447 41059714 38404475 a g 0.388 0.932 0.388 0.339 0.213 0.447 0.448 0.341 0.277 0.768
690971 99 C_765227 41025330 38370091 g t      0.281 0.885     
528854 100 C_1588417 41006873 38351634 a g 0.106 0.230 0.098 0.488 0.479 0.990    0.063 0.644
323495 101 C_1588405 40983252 38328013 g a 0.316 0.182 0.342 0.568 0.208 0.001 0.396 0.135 0.443 0.407
2593595 102 C_3256885 40965010 38309771 a g 0.124 0.007 0.054 0.672 0.156 0.002 0.135 0.883 0.177 <.0001
324075 103 C_3256881 40935288 38280049 a g 0.171 0.717 0.195 0.063 0.115 0.370 0.156 0.365 0.330 0.558
2290041 104 C_15883310 40856085 38200846 c t 0.012 0.913    0.302 0.103 0.031 0.823   
1078523 105 C_2160077 40821525 38166286 a g 0.480 0.158 0.370 0.650 0.135 0.883 0.478 0.369 0.474 0.075
752313 106 C_1075621 40810589 38155350 t c 0.363 0.314 0.422 0.851 0.292 0.954 0.406 0.250 0.351 0.251
7359598 107 C_3256867 40806234 38150996 c t 0.386 0.073 0.440 0.674 0.135 0.883 0.438 0.486 0.383 0.243
2271027 108 C_15959277 40779567 38124328 c t      0.065 0.636 0.031 0.823   
7214055 109 C_1441435 40761936 38106697 c g 0.149 0.109 0.008 0.948 0.385 0.003 0.031 0.823 0.021 0.882
9766 110 C_1441436 40761606 38106367 g a 0.353 0.219 0.433 0.700 0.292 0.954 0.406 0.250 0.344 0.823
1553469 111 C_7529639 40751527 38096288 a c 0.065 0.248 0.058 0.061 0.031 <.0001    0.202 0.943
2271029 112 C_1125369 40744687 38089448 c a 0.405 0.009 0.350 0.444 0.375 0.441 0.385 0.937 0.402 0.117
3760384 113 C_1441438 40744216 38088977 a c 0.359 0.020 0.392 0.666 0.447 0.716 0.385 0.937 0.458 0.023
2292749 114 C_1441444 40727349 38072110 c t 0.217 0.219 0.383 0.518 0.192 0.794 0.375 0.878 0.128 0.316
Number of polymorphic loci 83   80   99   71   82  
Number of SNPs with maf<0.05 11   13   14   6   17  
Mean maf 0.305   0.269   0.181   0.327   0.287  
  1. a April 2003 (Build 33) Position
  2. b March 2006 (Build 36.1) Position
  3. c Com Allele = Common allele
  4. d Min Allele = Minor allele
  5. e maf = Minor allele frequency
  6. f Population private SNPs are shown underlined
  7. gNA= Not Applicable – not in dbSNP
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BMC Genomic Data

ISSN: 2730-6844

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