Variant report

Variant	rs16839881
Chromosome Location	chr1:196374780-196374781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:196372518..196376500-chr1:196378398..196382162,4	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10737671	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs10737676	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs10737678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10754192	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs10754194	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10801536	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10922057	1.00[CHB][hapmap]
rs10922081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11806479	1.00[CHB][hapmap]
rs12072649	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs12407653	1.00[JPT][hapmap]
rs1339947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1339949	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1339951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1416960	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1416966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1416970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1416971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1538683	0.85[CEU][hapmap]
rs1556961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1571489	1.00[JPT][hapmap]
rs16829753	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839668	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839682	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839685	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839693	0.90[AMR][1000 genomes]
rs16839698	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs16839716	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839751	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839758	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839763	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839771	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839782	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839795	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839822	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16839832	0.82[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16839841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16839872	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]
rs16839878	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]
rs16839884	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]
rs16839886	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]
rs16839905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639647	1.00[AFR][1000 genomes]
rs2296269	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs2335907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs41451950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4294368	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4316314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4405100	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs4518841	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs4562566	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs4601531	0.85[CEU][hapmap]
rs4614205	1.00[JPT][hapmap]
rs4633231	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4658042	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6670223	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6680722	0.82[EUR][1000 genomes]
rs6688468	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6702610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7531491	1.00[JPT][hapmap]
rs7541165	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544202	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7544266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552170	0.82[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469680	chr1:196259846-196419016	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv482746	chr1:196259846-196419016	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv872953	chr1:196286639-196411281	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872954	chr1:196304863-196387809	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv872955	chr1:196339655-196374780	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv548742	chr1:196339655-196391866	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv872956	chr1:196339655-196411281	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv872957	chr1:196347066-196411281	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196343400-196377200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr1:196356400-196375600	Weak transcription	Fetal Kidney	kidney
3	chr1:196358000-196393800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:196370200-196375800	Weak transcription	Fetal Lung	lung
5	chr1:196370400-196376000	Weak transcription	Ovary	ovary
6	chr1:196370600-196375600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:196370800-196376800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:196371000-196376000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:196371200-196376600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:196372200-196375200	Weak transcription	HepG2	liver
11	chr1:196372600-196383800	Weak transcription	Liver	Liver
12	chr1:196373600-196376000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:196373800-196376600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:196374000-196375800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:196374000-196375800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:196374000-196375800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:196374000-196375800	Weak transcription	NH-A	brain
18	chr1:196374000-196376400	Weak transcription	HSMM	muscle
19	chr1:196374000-196376600	Weak transcription	HUVEC	blood vessel
20	chr1:196374200-196376000	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links