Variant report

Variant	rs17009261
Chromosome Location	chr3:21718522-21718523
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:21709988..21712111-chr3:21717387..21720312,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10510515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510516	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11129015	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11710740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712782	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs11718610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152283	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635315	1.00[AFR][1000 genomes]
rs17009232	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17009250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17009271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55877448	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66491866	0.91[EUR][1000 genomes]
rs73037288	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73040075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73042114	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73042122	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73042130	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73042147	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73042185	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73046212	1.00[AFR][1000 genomes]
rs73046229	1.00[AFR][1000 genomes]
rs73046249	1.00[AFR][1000 genomes]
rs73046250	1.00[AFR][1000 genomes]
rs73046267	1.00[AFR][1000 genomes]
rs7615960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9310651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310652	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9853494	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859103	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859423	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9863531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9870622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883454	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010460	chr3:21516810-21839871	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834631	chr3:21612283-21763887	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1007048	chr3:21666807-21865229	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv536516	chr3:21666807-21865229	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv527771	chr3:21716235-21726363	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21707400-21719600	Weak transcription	Fetal Lung	lung
2	chr3:21707800-21719800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:21708200-21719800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:21710000-21719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:21710000-21724400	Weak transcription	Left Ventricle	heart
6	chr3:21711200-21719600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:21714200-21719600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:21715000-21728600	Weak transcription	Psoas Muscle	Psoas
9	chr3:21717400-21718600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:21717400-21718600	Active TSS	Aorta	Aorta
11	chr3:21718400-21718600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:21718400-21718800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:21718400-21718800	Enhancers	Fetal Stomach	stomach
14	chr3:21718400-21719000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links