SNP Report

Basic Info
Name |
rs6279
dbSNP
Ensembl
|
Location |
11:113410351 - 113410351(+) |
Variant Seq |
C |
Ancestral Allele |
G |
Ref Seq |
G |
Minor Allele Frequence |
0.478235 |
Annotation |
downstream_gene_variant; 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant
|
Variant Effect |
downstream_gene_variant(ENST00000538967, ENST00000539420, ENST00000540600, ENST00000535984); 3_prime_UTR_variant(ENST00000544518, ENST00000542968, ENST00000346454, ENST00000362072); intron_variant(ENST00000546284); non_coding_transcript_variant(ENST00000546284)
|
SIFT Annotation |
tolerated
|
SIFT Variant Effect |
tolerated(ENST00000538967, ENST00000544518, ENST00000362072, ENST00000542968)
|
PolyPhen Annotation |
benign
|
PolyPhen Variant Effect |
benign(ENST00000538967, ENST00000544518, ENST00000362072, ENST00000542968)
|
rSNP? |
Yes
Link in rVarBase
|
Related Regulatory Elements |
n/a
|
Chromatin State |
Weak transcription
|
No. of Marker's Association Results |
1 (Positive: 0; Negative: 1; Trend: 0) |
Source |
Literature |

SNP related association results

SNP related genes (count: 1)

SNPs in LD with rs6279 (count: 28)
The LD data used here is based on 1000 Genome Phase I. LD SNP pairs were selected with a threshold r2<=0.8.
Literature-origin SNPs (count: 1)

|
rs_ID |
Annotation |
No. of Association Results(Positive/Negative/Trend) |
r2[population] |
rs1124492
|
downstream_gene_variant(ENST00000539420, ENST00000535984, ENST00000540600); non_coding_transcript_exon_variant(ENST00000546284); intron_variant(ENST00000544518, ENST00000542968, ENST00000346454, ENST00000538967, ENST00000362072); non_coding_transcript_variant(ENST00000546284) |
1(0/1/0)
|
0.8566[ASN] |
LD-proxies (count: 27)

rs_ID |
Literature-origin SNPs with LD |
Annotation |
r2[population] |
rs2587543
|
rs6279
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs2005313
|
rs6279
|
upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9314[ASN] |
rs11214602
|
rs6279
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9859[ASN] |
rs6275
|
rs6279
|
synonymous_variant; downstream_gene_variant |
0.9653[ASN] |
rs2587552
|
rs6279
|
downstream_gene_variant; upstream_gene_variant |
0.9789[ASN] |
rs4938016
|
rs6279
|
downstream_gene_variant; missense_variant |
0.9580[ASN] |
rs2859544
|
rs6279
|
downstream_gene_variant; upstream_gene_variant |
0.9789[ASN] |
rs2587550
|
rs6279
|
downstream_gene_variant; upstream_gene_variant |
0.9789[ASN] |
rs1124493
|
rs6279
|
downstream_gene_variant; non_coding_transcript_exon_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs2471856
|
rs4586205
rs6279
|
upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9039[ASN] |
rs61492892
|
rs1124492
rs6279
|
upstream_gene_variant; intron_variant |
0.8132[ASN] |
rs2734841
|
rs6279
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs2734842
|
rs6279
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs1003641
|
rs6279
|
downstream_gene_variant; upstream_gene_variant |
0.9789[ASN] |
rs11214598
|
rs6279
|
intron_variant; NMD_transcript_variant |
0.9580[ASN] |
rs2245805
|
rs6279
|
downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9314[ASN] |
rs6276
|
rs6279
|
downstream_gene_variant; 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs7122228
|
rs6279
|
downstream_gene_variant; intron_variant |
0.9580[ASN] |
rs12224538
|
rs1124492
rs6279
|
upstream_gene_variant; intron_variant |
0.8132[ASN] |
rs2859543
|
rs6279
|
downstream_gene_variant; upstream_gene_variant |
0.9789[ASN] |
rs4590907
|
rs1124492
rs6279
|
upstream_gene_variant; intron_variant |
0.8132[ASN] |
rs1076562
|
rs6279
|
upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9244[ASN] |
rs4938014
|
rs1124492
rs6279
|
intron_variant; NMD_transcript_variant |
0.8190[ASN] |
rs2002453
|
rs6279
|
upstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9314[ASN] |
rs2511521
|
rs6279
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
0.9380[ASN] |
rs2242592
|
rs6279
|
downstream_gene_variant; intron_variant; non_coding_transcript_variant |
1.0000[ASN] |
rs2859545
|
rs6279
|
downstream_gene_variant; upstream_gene_variant |
0.9649[ASN] |

SNP related eQTL (count: 1)