Variant report

Variant	rs12077962
Chromosome Location	chr1:98446194-98446195
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10747488	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10747489	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10747490	0.82[ASN][1000 genomes]
rs10747491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10747492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875111	0.82[ASN][1000 genomes]
rs10875112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10875120	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875121	0.88[ASN][1000 genomes]
rs11165920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11165921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11165934	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165935	0.88[ASN][1000 genomes]
rs11165937	0.88[ASN][1000 genomes]
rs11165938	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165939	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165940	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1198591	1.00[JPT][hapmap]
rs1198592	1.00[JPT][hapmap]
rs1198593	1.00[JPT][hapmap]
rs1198594	1.00[JPT][hapmap]
rs12062845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12067567	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068763	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12069474	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12071067	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12072739	0.88[ASN][1000 genomes]
rs12073487	0.88[ASN][1000 genomes]
rs12077442	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12089031	0.88[ASN][1000 genomes]
rs12094520	0.81[AFR][1000 genomes]
rs12406713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17379561	1.00[JPT][hapmap]
rs1801265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2660303	1.00[JPT][hapmap]
rs2660304	1.00[JPT][hapmap]
rs28582591	0.88[ASN][1000 genomes]
rs28641479	0.88[ASN][1000 genomes]
rs36028749	0.81[AFR][1000 genomes]
rs41285694	0.84[ASN][1000 genomes]
rs4246515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4246516	0.88[ASN][1000 genomes]
rs4274102	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4294451	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4322261	0.82[ASN][1000 genomes]
rs4372296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4379706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4394693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs4394694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4421623	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4423049	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4456128	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4495746	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4506495	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4523551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4523552	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs45522136	0.81[ASN][1000 genomes]
rs4598523	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4970719	0.88[ASN][1000 genomes]
rs4970720	0.82[ASN][1000 genomes]
rs4970721	0.82[ASN][1000 genomes]
rs4970722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4970723	0.82[ASN][1000 genomes]
rs4970725	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56732321	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57468345	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61785881	0.88[ASN][1000 genomes]
rs61785882	0.81[ASN][1000 genomes]
rs61785883	0.88[ASN][1000 genomes]
rs61785886	0.81[ASN][1000 genomes]
rs61787782	0.88[ASN][1000 genomes]
rs61787819	0.82[ASN][1000 genomes]
rs61787820	0.82[ASN][1000 genomes]
rs61789075	0.88[ASN][1000 genomes]
rs61789077	0.88[ASN][1000 genomes]
rs61789078	0.88[ASN][1000 genomes]
rs61789079	0.88[ASN][1000 genomes]
rs61789082	0.88[ASN][1000 genomes]
rs6604093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs6604098	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6658412	0.88[ASN][1000 genomes]
rs6664489	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6677116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6692580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6703588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72963738	0.88[ASN][1000 genomes]
rs7415086	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7418577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7524038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7526108	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs9285628	0.88[ASN][1000 genomes]
rs9324374	0.82[ASN][1000 genomes]
rs9324378	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9324379	0.88[ASN][1000 genomes]
rs9659380	0.88[ASN][1000 genomes]
rs9661794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9662232	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9662719	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9662870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9727548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs9727976	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9729190	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9729897	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9887831	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9887848	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1009621	chr1:98435638-98599284	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv871230	chr1:98436232-98564736	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98409600-98455000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:98438000-98460200	Weak transcription	HSMM	muscle
3	chr1:98440200-98462000	Weak transcription	NHDF-Ad	bronchial
4	chr1:98446000-98446200	Enhancers	Brain Substantia Nigra	brain

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