Variant report

Variant	rs1001788
Chromosome Location	chr3:61171806-61171807
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	chr3:61167426..61169661-chr3:61171203..61172847,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10049007	0.96[ASN][1000 genomes]
rs10049287	0.96[ASN][1000 genomes]
rs10049452	0.96[ASN][1000 genomes]
rs10049454	0.96[ASN][1000 genomes]
rs11707984	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11712122	0.96[ASN][1000 genomes]
rs12053817	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12635622	0.96[ASN][1000 genomes]
rs13099397	0.82[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs13320646	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13323296	0.92[ASN][1000 genomes]
rs1371095	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1473644	0.83[ASN][1000 genomes]
rs1550343	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1554601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1866433	1.00[JPT][hapmap]
rs1916802	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1966136	1.00[JPT][hapmap]
rs1969420	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2118811	0.96[ASN][1000 genomes]
rs2886377	0.88[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4309721	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4535219	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4688295	1.00[ASN][1000 genomes]
rs4688310	0.98[ASN][1000 genomes]
rs56076618	0.96[ASN][1000 genomes]
rs61275795	0.93[ASN][1000 genomes]
rs6445196	0.98[ASN][1000 genomes]
rs6787511	0.92[ASN][1000 genomes]
rs6807748	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7631101	0.96[ASN][1000 genomes]
rs7631246	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7636682	0.96[ASN][1000 genomes]
rs7641177	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7647122	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7653719	0.84[ASN][1000 genomes]
rs9814044	0.96[ASN][1000 genomes]
rs9816087	0.89[ASN][1000 genomes]
rs9839082	0.96[ASN][1000 genomes]
rs9844741	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9850125	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9851485	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9855716	0.82[JPT][hapmap]
rs9857606	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs9861713	0.92[ASN][1000 genomes]
rs9871451	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9871598	0.96[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1001788	ID2B	cis	cerebellum	SCAN

Chromatin state (count:10 , 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	chr3:61158800-61172000	Weak transcription	Pancreas	Pancrea
3	chr3:61159600-61172000	Weak transcription	Gastric	stomach
4	chr3:61161000-61186000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:61166400-61177800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:61167400-61172000	Weak transcription	Psoas Muscle	Psoas
7	chr3:61168400-61179000	Weak transcription	HepG2	liver
8	chr3:61168600-61180600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:61169200-61172000	Weak transcription	GM12878-XiMat	blood
10	chr3:61171400-61172200	Weak transcription	Ovary	ovary

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