Variant report

Variant	rs898611
Chromosome Location	chr12:57163316-57163317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57151540..57154477-chr12:57162511..57165120,2	K562	blood:
2	chr12:57157079..57158624-chr12:57160965..57163769,2	MCF-7	breast:
3	chr12:57156599..57160175-chr12:57160650..57163497,3	K562	blood:
4	chr12:57161853..57164253-chr12:57165947..57168097,2	MCF-7	breast:
5	chr12:57115492..57120311-chr12:57159209..57164000,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196531	Chromatin interaction
ENSG00000025423	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1026565	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459246	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747770	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783796	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876916	0.95[CEU][hapmap];0.93[CHB][hapmap]
rs10876918	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1107479	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap]
rs11171914	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs11171951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171956	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171986	0.81[JPT][hapmap]
rs1131514	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12227117	0.88[ASN][1000 genomes]
rs12229457	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs12828563	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1466382	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1563896	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs1975875	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1979325	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2035081	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2035082	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255074	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs2290893	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs2290894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2926743	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2926747	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2926748	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2950387	0.80[CHB][hapmap];0.82[TSI][hapmap]
rs2950390	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2958123	0.95[CEU][hapmap];0.93[CHB][hapmap]
rs2958127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2958130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958132	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958134	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2958148	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2958149	0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2958153	0.93[CHB][hapmap];0.84[CHD][hapmap]
rs2958154	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2958155	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap]
rs3214051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4277148	0.81[JPT][hapmap]
rs4759254	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs4759256	0.96[ASN][1000 genomes]
rs4788	0.88[ASN][1000 genomes]
rs4902	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7137749	0.84[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7313074	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7966391	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7967600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978685	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7980317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941207	0.86[CHB][hapmap]
rs9634246	0.93[CHB][hapmap];0.81[CHD][hapmap]

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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1794914	chr12:57119236-57195379	Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv826382	chr12:57151464-57208607	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs898611	PRIM1	cis	multi-tissue	Pritchard
rs898611	RBMS2	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57155800-57166000	Weak transcription	Right Atrium	heart
2	chr12:57156400-57179400	Weak transcription	Spleen	Spleen
3	chr12:57157600-57163600	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:57157800-57171000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:57158600-57179200	Weak transcription	HSMMtube	muscle
6	chr12:57159800-57164000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:57160400-57163600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:57160400-57168400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:57160600-57163400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:57160600-57163600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:57160600-57163600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:57160800-57164000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:57160800-57179400	Weak transcription	Lung	lung
14	chr12:57161000-57165200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:57161000-57165400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:57161800-57163800	Enhancers	HepG2	liver
17	chr12:57163200-57164000	Enhancers	Liver	Liver

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