Variant report

Variant	rs12072655
Chromosome Location	chr1:86884539-86884540
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	chr1:86884451..86885554-chr1:86967355..86968572,5	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10782571	0.94[ASN][1000 genomes]
rs10873771	0.88[ASN][1000 genomes]
rs10873772	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs10873773	0.94[ASN][1000 genomes]
rs10873774	0.92[ASN][1000 genomes]
rs10873775	0.94[ASN][1000 genomes]
rs10873776	0.94[ASN][1000 genomes]
rs10873778	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs1116108	0.96[CEU][hapmap];0.81[CHD][hapmap]
rs1116109	0.96[ASN][1000 genomes]
rs11161803	0.90[ASN][1000 genomes]
rs11161804	0.90[ASN][1000 genomes]
rs11161805	0.94[ASN][1000 genomes]
rs11161807	0.94[ASN][1000 genomes]
rs11161811	0.98[ASN][1000 genomes]
rs11799437	0.95[CEU][hapmap];0.81[CHD][hapmap]
rs11802019	0.91[CEU][hapmap]
rs11810689	0.94[ASN][1000 genomes]
rs12031536	0.90[ASN][1000 genomes]
rs12033867	0.95[ASN][1000 genomes]
rs1407719	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs1407720	0.94[ASN][1000 genomes]
rs1413427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413429	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16908	0.96[CEU][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17372196	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1830675	0.88[ASN][1000 genomes]
rs1999600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[ASN][1000 genomes]
rs2031136	0.94[ASN][1000 genomes]
rs2093612	0.92[ASN][1000 genomes]
rs2181418	0.93[ASN][1000 genomes]
rs2210641	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273941	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2275000	0.90[ASN][1000 genomes]
rs2275001	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2390057	0.82[CEU][hapmap]
rs2390096	0.94[ASN][1000 genomes]
rs2390097	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[ASN][1000 genomes]
rs2390099	0.94[ASN][1000 genomes]
rs35173920	0.86[ASN][1000 genomes]
rs3737159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737672	0.96[CEU][hapmap];0.80[CHD][hapmap];0.88[MEX][hapmap]
rs3765986	0.91[CEU][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3945233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4534352	0.94[ASN][1000 genomes]
rs4656026	0.90[ASN][1000 genomes]
rs4656044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs58200516	0.94[ASN][1000 genomes]
rs6658025	0.92[ASN][1000 genomes]
rs6674140	0.94[ASN][1000 genomes]
rs6703576	0.94[ASN][1000 genomes]
rs67799288	0.94[ASN][1000 genomes]
rs7415758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515651	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7541004	0.86[ASN][1000 genomes]
rs7553685	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs956499	0.96[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12072655	GBP7	cis	cerebellum	SCAN
rs12072655	ODF2L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86882200-86885200	Weak transcription	Esophagus	oesophagus
2	chr1:86882200-86894800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:86882400-86885000	Weak transcription	NHEK	skin
4	chr1:86882400-86885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:86882400-86885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:86882400-86885200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:86882400-86885200	Weak transcription	Hela-S3	cervix
8	chr1:86883800-86884800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:86884000-86885000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:86884000-86885000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:86884000-86885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:86884200-86885200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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