Variant report

Variant	rs1403968
Chromosome Location	chr3:61172318-61172319
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	chr3:61167426..61169661-chr3:61171203..61172847,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10866044	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11130818	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11130819	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11707813	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711938	0.90[ASN][1000 genomes]
rs11716189	0.91[ASN][1000 genomes]
rs11720347	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11917930	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs11927024	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11927051	0.97[EUR][1000 genomes]
rs11929245	0.97[EUR][1000 genomes]
rs12492742	0.84[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs12494269	0.86[ASN][1000 genomes]
rs12494967	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs12629280	0.97[EUR][1000 genomes]
rs12632475	0.88[ASN][1000 genomes]
rs12633494	0.82[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs12637792	0.84[JPT][hapmap]
rs13087102	0.90[ASN][1000 genomes]
rs13323559	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1880218	0.86[ASN][1000 genomes]
rs2218088	1.00[EUR][1000 genomes]
rs28735912	0.86[ASN][1000 genomes]
rs2886260	0.89[ASN][1000 genomes]
rs4688135	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4688292	0.86[ASN][1000 genomes]
rs4688324	0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4688333	0.99[EUR][1000 genomes]
rs4688338	0.98[EUR][1000 genomes]
rs61440939	0.88[ASN][1000 genomes]
rs9820155	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9820332	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9823902	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs9841468	0.96[EUR][1000 genomes]
rs9864918	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs9870560	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9875228	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9875365	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9875504	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9875844	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9876185	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs9877396	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9877573	0.90[ASN][1000 genomes]
rs9879191	0.97[EUR][1000 genomes]
rs9879848	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs9881340	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9884072	0.86[AFR][1000 genomes]
rs9917837	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv590425	chr3:61132698-61186550	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1012435	chr3:61136874-61181318	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1014142	chr3:61136874-61184782	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61151200-61188000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61161000-61186000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:61166400-61177800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:61168400-61179000	Weak transcription	HepG2	liver
5	chr3:61168600-61180600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:61172000-61172400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:61172000-61172400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:61172000-61172400	Enhancers	Esophagus	oesophagus
9	chr3:61172000-61172400	Enhancers	Gastric	stomach
10	chr3:61172000-61172400	Enhancers	Pancreas	Pancrea
11	chr3:61172000-61172400	Enhancers	GM12878-XiMat	blood
12	chr3:61172200-61172400	Enhancers	Ovary	ovary

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