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Table 2 SNPs identified for various cohorts using the stringent filter (Part 1).

From: Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes

Cohort(s) SNP/identity
(degeneracy)
Chr: Pos. (hg17)
and orientation
Duplicon
length
Characterized genes and
pseudogenes in duplicons
CD rs4471699 16: 30.2 M→ 147 kb SULT1A3, GIYD2, BOLA2, IMAA, CORO1A
  99.6% 16: 29.4 M→ 146 kb SULT1A3, GIYD2, BOLA2, IMAA, MLAS
  98.1% 16: 21.8 M→ 41 kb [UQCRC2]
  98.0% 16: 22.3 M← 42 kb [NPIPL3]
  98.0% 16: 21.3 M→ 42 kb IMAA, [NPIPL3]
  97.1% 16: 18.8 M→ 75 kb SMG1
RA rs669980 9: 0.2 M→ 193 kb CBWD1, FOXD4, FAM138A, WASH1, [DOCK8]
  98.9% (F) 2: 114 M← 189 kb CBWD2, FOX4DL1, FAM138B, WASH2P, [RABL2A]
CAD, T2D rs10502407 18: 10.6 M→ 52 kb -
  97.9% 18: 12.2 M← 64 kb [CIDEA]
CAD rs12134625 1: 78 M→ 931 -
  97.0% 1: 24 M← 932 FUSIP1
BD, CAD rs9551988 13: 19.2 M→ 2.6 kb PSPC1
HT 96.2% (F) 13: 18.7 M→ 2.8 kb [TUBA3C]
HT rs935019 2: 127,162 K→ 3.6 kb GYPC
  95.3% (F) 2: 127,166 K→ 3.5 kb GYPC
HT rs12227938 12: 37 M→ 154 kb ALG10B
  95.3% (P) 12: 34 M→ 127 kb ALG10
T2D SNP_A-1797773 16: 45 M→ 14 kb VPS35, [ORC6L]
  94.8% (F) 16: 34 M← 16 kb -
T1D rs12381130 16: 5 M→ 88 kb ALG1, FAM86A
  94.7% 3: 127 M← 76 kb ALG1L
  94.6% 11: 67 M→ 79 kb -
  94.6% 11: 71 M← 40 kb FAM86C, [DEFB108B]
  94.5% 11: 3 M→ 91 kb [ZNF195]
  94.3% 3: 76 M→ 44 kb [FAM86D]
  94.0% 4: 9 M← 120 kb -
  93.9% 3: 131 M→ 44 kb -
  93.9% 4: 4 M→ 53 kb -
  93.7% 12: 8 M→ 53 kb [FAM90A1]
  93.6% 8: 12 M→ 41 kb [FAM86B1]
  93.5% 8: 8 M← 63 kb -
  1. Multiple almost-contiguous segmental duplications are treated as a single large duplicon (intervening sequence is included in the length). The table includes only duplicons with at least 85% identity to the region containing the SNP. Duplicons with identical flanking sequence to the SNP are labeled as fully degenerate (F); duplicons with partial degeneracy are labeled (P). Characterized genes are listed if they occur within a duplicon. Genes in square brackets are outside the duplicon, but the duplicon is at most 30 kb upstream of the gene. Genes for a SNP are italicized if the SNP is within that gene, or if the SNP maps to a position within that gene in the duplicon.