Table 2.
Identified ANXA1 novel variants and SNPs absent in controls
| Genomic position (hg18) | Nucleotide change | Amino acid change | Location | Transcript | Novel/SNP | Frequency cases | Genotype | In silico analysis | PhastCons (primates) |
|---|---|---|---|---|---|---|---|---|---|
| 74956445 |
G > A |
– |
5' of the gene |
ENST00000257497 |
Novel1 |
0.002 |
Homo |
TFBS abolished: VDR, CAR, PXR; NF-Y, C-myb, Crx; TFBS created: HNF6, Nkx6-2, OTX, CdxA |
0.48 |
| 74956718 |
CTA > Del.CTA |
– |
Intron 1–2 |
ENST00000257497 |
Novel1 |
0.002 |
Het |
- |
0.23 |
| 74962617 |
C > T |
– |
5'UTR |
ENST00000376911 |
rs27951151 |
0.002 |
Het |
- |
0.014 |
| 74964058 |
T > C |
– |
intron 3–4 |
ENST00000257497 |
rs101143501 |
0.002 |
Het |
splice-site SNP (ENSEMBL), ISRE down (pfSNP) |
0.81 |
| 74972178 |
G > A |
– |
intron 10–11 |
ENST00000257497 |
Novel1 |
0.005 |
Het |
– |
0.1 |
| 74972626 |
T > G |
– |
Intron 11–12 |
ENST00000257497 |
Novel1 |
0.002 |
Het |
– |
0.18 |
| 74973075 |
G > C |
– |
Intron 11–12 |
ENST00000257497 |
rs101196051 |
0.002 |
Het |
– |
0.11 |
| 74973545 |
T > C |
– |
Intron 11–12 |
ENST00000257497 |
Novel1 |
0.002 |
Het |
– |
NA |
| 74975361 |
G > A |
– |
3' (intergenic) |
– |
Novel |
0.002 |
Het |
– |
0.05 |
| 74975609 |
T > A |
– |
3' (intergenic) |
– |
Novel |
0.002 |
Het |
– |
0.78 |
| 74975645 |
T > C |
– |
3' (intergenic) |
– |
rs149272288 |
0.001 |
Het |
– |
0.014 |
| 74975873 |
C > T |
– |
3' (intergenic) |
– |
rs9792653 |
0.051 |
Het |
– |
NA |
| 74975882 |
C > T |
– |
3' (intergenic) |
– |
rs143327464 |
0.004 |
Het |
– |
NA |
| 74976171 |
C > T |
– |
3' (intergenic) |
– |
rs113627562 |
0.004 |
Het |
– |
NA |
| 74976222 |
A > G |
– |
3' (intergenic) |
– |
rs72737044 |
0.017 |
Het/Homo |
– |
0.18 |
| 74976536 |
C > T |
– |
3' (intergenic) |
– |
Novel |
0.001 |
Het |
– |
0.03 |
| 74976574 |
T > C |
– |
3' (intergenic) |
– |
rs78798837 |
0.002 |
Het |
– |
NA |
| 74977215 |
T > C |
– |
3' (intergenic) |
– |
Novel |
0.001 |
Het |
– |
0.006 |
| 74977218 |
C > T |
– |
3' (intergenic) |
– |
rs146061737 |
0.001 |
Het |
– |
0.003 |
| 74977655 |
A > G |
– |
3' (intergenic) |
– |
rs114240435 |
0.002 |
Het |
– |
0 |
| 74977680 |
C > A |
– |
3' (intergenic) |
– |
rs114833327 |
0.001 |
Het |
– |
NA |
| 74977840 |
G > A |
– |
3' (intergenic) |
– |
rs11143512 |
0.465 |
Het/Homo |
– |
NA |
| 74977852 |
A > G |
– |
3' (intergenic) |
– |
Novel |
0.001 |
Het |
– |
0.01 |
| 74977888 |
C > G |
– |
3' (intergenic) |
– |
rs17653109 |
0.089 |
Het/Homo |
– |
0.07 |
| 74977928 |
C > T |
– |
3' (intergenic) |
– |
rs75260654 |
0.023 |
Het |
– |
NA |
| 74977965 |
C > G |
– |
3' (intergenic) |
– |
Novel |
0.001 |
Het |
– |
0.08 |
| 74977981 |
C > T |
– |
3' (intergenic) |
– |
rs4443724 |
1 |
Homo |
– |
0.003 |
| 74977990 |
C > T |
– |
3' (intergenic) |
– |
rs116224215 |
0.007 |
Het |
– |
NA |
| 74978003 | C > T | – | 3' (intergenic) | – | rs4285546 | 0.04 | Het/Homo | – | 0.003 |
1Absent in a panel of 262 control individuals; Homo, homozygous; Het, heterozygous; TFBS, transcription factor binding site; NA, not available.