Variant report

Variant	rs1465685
Chromosome Location	chr2:56186471-56186472
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	chr2:56001464..56004424-chr2:56185372..56187665,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10185077	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10192259	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125611	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12472832	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13431149	0.97[ASN][1000 genomes]
rs1432560	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1432561	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1432563	0.98[ASN][1000 genomes]
rs1432564	0.97[ASN][1000 genomes]
rs1583266	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1583267	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1897478	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278366	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2868984	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34552760	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3972318	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4258837	0.92[CHB][hapmap]
rs4453721	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4635565	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672080	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672081	0.98[ASN][1000 genomes]
rs4672082	0.98[ASN][1000 genomes]
rs55805406	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545531	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704991	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721145	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6724998	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6733881	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6733889	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747490	0.97[ASN][1000 genomes]
rs724539	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724540	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7422809	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7561395	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561417	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7564964	0.98[ASN][1000 genomes]
rs981037	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv874161	chr2:56154316-56203798	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
4	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56180000-56188800	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:56183800-56186600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr2:56184200-56186600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:56184400-56186600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:56184400-56186600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:56184800-56186800	Enhancers	HMEC	breast
7	chr2:56185000-56187000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:56185200-56186600	Enhancers	HSMMtube	muscle
9	chr2:56185800-56186600	Enhancers	Osteobl	bone
10	chr2:56185800-56186800	Enhancers	Hela-S3	cervix
11	chr2:56185800-56187400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:56185800-56188400	Weak transcription	Adipose Nuclei	Adipose
13	chr2:56186000-56186600	Enhancers	A549	lung
14	chr2:56186000-56186600	Enhancers	HSMM	muscle
15	chr2:56186000-56186800	Enhancers	NHEK	skin
16	chr2:56186000-56187400	Weak transcription	Stomach Mucosa	stomach
17	chr2:56186200-56188200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:56186200-56188400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:56186400-56188200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:56186400-56188400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:56186400-56193200	Weak transcription	NH-A	brain

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