Variant report

Variant	rs12713098
Chromosome Location	chr2:50626192-50626193
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:50621939..50623486-chr2:50624372..50627015,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1005431	0.83[MEX][hapmap]
rs10181522	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10184843	0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap]
rs10188271	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10191195	0.84[CHB][hapmap]
rs10191261	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10201390	0.90[JPT][hapmap]
rs10203960	0.90[JPT][hapmap]
rs10205311	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10209627	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10210660	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10490228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12465784	0.90[ASN][1000 genomes]
rs12467043	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12475979	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs12713097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12994492	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13005521	0.82[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs13014058	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13014624	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13032292	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13032775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13382506	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13392422	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap]
rs13421278	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs13430295	0.90[ASW][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap]
rs13430435	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1402124	0.90[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs1402128	0.87[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1520439	0.83[MEX][hapmap]
rs1520443	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1520446	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1520449	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1533692	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17040569	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17040577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17040600	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap]
rs1818714	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1818715	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1818716	0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1851015	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs2351517	0.90[JPT][hapmap]
rs4638832	0.80[ASN][1000 genomes]
rs57564327	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6709416	1.00[JPT][hapmap]
rs6711307	0.83[MEX][hapmap]
rs6738086	0.83[MEX][hapmap]
rs6756219	0.83[MEX][hapmap]
rs7567375	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9309182	0.83[MEX][hapmap]
rs939402	0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12713098	MCFD2	cis	parietal	SCAN
rs12713098	LHCGR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50624400-50626200	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr2:50624400-50628600	Weak transcription	Stomach Mucosa	stomach
3	chr2:50624400-50629200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:50624800-50626200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr2:50625200-50626800	Enhancers	Brain Germinal Matrix	brain
6	chr2:50625800-50626400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:50626000-50626200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:50626000-50626800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:50626000-50629000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:50626000-50629400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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