Variant report

Variant	rs9662232
Chromosome Location	chr1:98400439-98400440
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10747488	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10747489	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs10747490	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10747491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10747492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10875111	0.88[ASN][1000 genomes]
rs10875112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10875113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10875118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10875120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875121	0.82[ASN][1000 genomes]
rs11165920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11165921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11165934	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165935	0.82[ASN][1000 genomes]
rs11165937	0.82[ASN][1000 genomes]
rs11165938	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165939	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165940	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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];0.88[ASN][1000 genomes]
rs12067567	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12067700	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12068763	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12069474	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071067	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12072739	0.82[ASN][1000 genomes]
rs12073487	0.82[ASN][1000 genomes]
rs12077442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12077962	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12089031	0.82[ASN][1000 genomes]
rs12406713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17379561	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1801265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2660303	1.00[JPT][hapmap]
rs2660304	1.00[JPT][hapmap]
rs28582591	0.82[ASN][1000 genomes]
rs28641479	0.82[ASN][1000 genomes]
rs4246515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4246516	0.82[ASN][1000 genomes]
rs4274102	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4294451	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4322261	0.88[ASN][1000 genomes]
rs4372296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4378243	0.94[ASN][1000 genomes]
rs4379706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4394693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4394694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4399192	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4421623	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4423049	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4456128	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478846	0.94[ASN][1000 genomes]
rs4495746	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4506495	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4523551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4523552	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4546957	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4598523	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970719	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4970720	0.88[ASN][1000 genomes]
rs4970721	0.88[ASN][1000 genomes]
rs4970722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4970723	0.88[ASN][1000 genomes]
rs4970725	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56732321	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57468345	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61785881	0.82[ASN][1000 genomes]
rs61785883	0.82[ASN][1000 genomes]
rs61787782	0.82[ASN][1000 genomes]
rs61787783	0.82[ASN][1000 genomes]
rs61787784	0.82[ASN][1000 genomes]
rs61787785	0.82[ASN][1000 genomes]
rs61787819	0.88[ASN][1000 genomes]
rs61787820	0.88[ASN][1000 genomes]
rs61787823	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61787824	0.88[ASN][1000 genomes]
rs61787826	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61787827	0.88[ASN][1000 genomes]
rs61787828	0.88[ASN][1000 genomes]
rs61787829	0.94[ASN][1000 genomes]
rs61787830	0.94[ASN][1000 genomes]
rs61789075	0.82[ASN][1000 genomes]
rs61789077	0.82[ASN][1000 genomes]
rs61789078	0.82[ASN][1000 genomes]
rs61789079	0.82[ASN][1000 genomes]
rs61789082	0.82[ASN][1000 genomes]
rs6604093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6604098	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658412	0.82[ASN][1000 genomes]
rs6664489	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6677116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6692580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs6703588	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72963738	0.82[ASN][1000 genomes]
rs7415086	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7418577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7524038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7526108	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9285628	0.82[ASN][1000 genomes]
rs9324374	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9324378	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9324379	0.82[ASN][1000 genomes]
rs9659380	0.82[ASN][1000 genomes]
rs9661794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9662719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9662870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9727548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9727976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9729190	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9729897	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9887831	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9887848	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98391000-98402200	Weak transcription	Brain Anterior Caudate	brain
2	chr1:98391200-98402600	Weak transcription	HSMM	muscle
3	chr1:98398200-98402000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:98398200-98402000	Weak transcription	Brain Substantia Nigra	brain
5	chr1:98398600-98401400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:98399000-98401400	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:98399000-98402200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:98399600-98401600	Enhancers	Dnd41	blood
9	chr1:98400000-98400600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:98400000-98400600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:98400400-98407000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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