Variant report

Variant	rs2932583
Chromosome Location	chr1:151931300-151931301
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151925413..151928425-chr1:151930738..151934740,3	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1038747	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10494270	0.90[CHB][hapmap]
rs1060870	0.83[AMR][1000 genomes]
rs10788817	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10788818	0.88[ASN][1000 genomes]
rs10788820	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11204914	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11204915	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11204922	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11589720	0.98[ASN][1000 genomes]
rs12067594	0.84[AMR][1000 genomes]
rs12083193	0.86[CHB][hapmap]
rs12116923	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12562586	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1387833	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1490189	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1532133	0.82[CHB][hapmap]
rs16833668	0.95[CHB][hapmap]
rs16833728	0.91[CHB][hapmap]
rs16833743	0.82[CHB][hapmap]
rs1907040	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2130525	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2279501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2337689	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2338019	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2338201	0.83[AMR][1000 genomes]
rs2338209	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932565	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932570	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2932576	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2932577	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2932579	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2932581	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932586	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932590	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999506	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2999508	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999512	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999526	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999528	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999531	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999534	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2999539	0.85[JPT][hapmap]
rs2999541	0.82[ASN][1000 genomes]
rs2999542	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999544	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999545	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2999546	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3007670	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3007685	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3007691	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007708	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3007711	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3791153	0.82[CHB][hapmap]
rs4845409	0.82[ASN][1000 genomes]
rs4845713	0.84[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6587635	0.86[CHB][hapmap]
rs6587636	0.86[CHB][hapmap]
rs6587637	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs6587638	0.85[CHB][hapmap]
rs6587640	0.86[CHB][hapmap]
rs6662611	0.86[CHB][hapmap]
rs6663064	0.95[CHB][hapmap]
rs6678672	0.86[CHB][hapmap]
rs6685187	0.80[JPT][hapmap];0.80[AMR][1000 genomes]
rs6686874	0.95[CHB][hapmap]
rs6698740	0.83[AMR][1000 genomes]
rs6703465	0.86[CHB][hapmap]
rs7535002	0.91[CHB][hapmap]
rs7541099	0.91[CHB][hapmap]
rs7542137	0.84[AMR][1000 genomes]
rs902313	0.91[CHB][hapmap]
rs9435963	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9435964	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs971887	0.86[CHB][hapmap]
rs9943221	0.91[CHB][hapmap]
rs9943251	0.88[CHB][hapmap]
rs9943281	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2932583	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2932583	THEM4	cis	multi-tissue	Pritchard
rs2932583	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2932583	THEM4	cis	Esophagus Muscularis	GTEx
rs2932583	THEM4	cis	Nerve Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151928000-151933000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:151930800-151940800	Weak transcription	NHDF-Ad	bronchial
3	chr1:151931200-151931600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:151931200-151932000	Enhancers	Primary monocytes fromperipheralblood	blood

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