Variant report

Variant	rs1934424
Chromosome Location	chr1:216080155-216080156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10746460	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12140657	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1575756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1934423	0.85[MEX][hapmap]
rs2576002	0.90[CHB][hapmap]
rs2764947	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2764951	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs4564111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs479826	0.90[CHB][hapmap]
rs489857	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs494350	0.85[ASN][1000 genomes]
rs519859	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs531780	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap]
rs542423	0.90[CHB][hapmap]
rs547022	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs553986	0.85[ASN][1000 genomes]
rs559921	0.90[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs568336	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs654702	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs687019	0.90[CHB][hapmap]
rs687693	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7544470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs927744	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv520724	chr1:216077764-216080155	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1934424	NEK2	cis	parietal	SCAN
rs1934424	USH2A	cis	parietal	SCAN

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216077800-216081000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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