Variant report

Variant	rs12712036
Chromosome Location	chr2:99462711-99462712
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	chr2:99461401..99464766-chr2:99483724..99486615,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10169003	0.87[EUR][1000 genomes]
rs10172158	0.84[EUR][1000 genomes]
rs10181972	0.87[EUR][1000 genomes]
rs10188156	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11123755	0.84[EUR][1000 genomes]
rs11887536	0.84[EUR][1000 genomes]
rs11893888	0.89[EUR][1000 genomes]
rs12468024	0.84[EUR][1000 genomes]
rs12712033	0.86[CHB][hapmap]
rs12712034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12712035	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12712038	0.84[EUR][1000 genomes]
rs12712039	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13004923	0.87[EUR][1000 genomes]
rs1356424	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1568213	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1581250	0.87[EUR][1000 genomes]
rs1581251	0.84[EUR][1000 genomes]
rs1878585	0.87[EUR][1000 genomes]
rs1983352	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2008648	0.86[AMR][1000 genomes]
rs2138082	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2280256	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs4263159	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs4850888	0.92[EUR][1000 genomes]
rs4851162	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4851163	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4851167	0.84[EUR][1000 genomes]
rs4851170	0.84[EUR][1000 genomes]
rs4851171	0.84[EUR][1000 genomes]
rs6542838	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs6542839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711022	0.89[EUR][1000 genomes]
rs6713991	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6714243	0.84[EUR][1000 genomes]
rs6717372	0.82[EUR][1000 genomes]
rs6719634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726156	0.88[EUR][1000 genomes]
rs6757099	0.83[EUR][1000 genomes]
rs7579189	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7608889	0.84[CEU][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs981601	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs981602	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
2	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
3	chr2:99450800-99462800	Weak transcription	Gastric	stomach
4	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:99456200-99473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:99461600-99464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:99462400-99463400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:99462400-99464800	Enhancers	NHDF-Ad	bronchial
9	chr2:99462400-99465000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:99462600-99463000	Enhancers	HSMM	muscle

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