Variant report

Variant	rs10789398
Chromosome Location	chr1:75018421-75018422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493546	0.81[CEU][hapmap];0.88[JPT][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs10890133	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10890136	0.85[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs10890137	0.89[CEU][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs10890138	0.81[CEU][hapmap]
rs11210488	0.88[EUR][1000 genomes]
rs11210489	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs12029405	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12074297	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12117493	0.81[CEU][hapmap]
rs1340987	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1424667	0.81[CEU][hapmap]
rs1563291	0.81[CEU][hapmap]
rs17548925	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1834189	0.81[CEU][hapmap]
rs3845350	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3845352	0.81[EUR][1000 genomes]
rs3845355	0.89[CEU][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs4123382	0.88[JPT][hapmap]
rs4650002	0.89[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs6660278	0.81[CEU][hapmap]
rs6671066	0.85[CEU][hapmap]
rs6700243	0.81[CEU][hapmap]
rs6701034	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs72675359	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72675360	0.90[EUR][1000 genomes]
rs9326117	0.80[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs9661462	0.89[CEU][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][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	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv830248	chr1:74962391-75144458	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1003356	chr1:74983681-75024938	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10789398	CRYZ	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75018400-75018600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:75018400-75019200	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links