Variant report

Variant	rs3019296
Chromosome Location	chr8:99929455-99929456
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10087533	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10092190	0.93[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs10094807	0.95[JPT][hapmap]
rs10096925	0.84[EUR][1000 genomes]
rs10098153	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10106041	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10108567	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10109066	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10955192	0.95[JPT][hapmap]
rs10955194	0.95[JPT][hapmap]
rs10955196	0.95[JPT][hapmap]
rs10955197	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10955202	0.84[EUR][1000 genomes]
rs11786078	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12547301	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12547849	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12550128	0.84[EUR][1000 genomes]
rs12680054	0.83[EUR][1000 genomes]
rs2922066	1.00[YRI][hapmap]
rs2922070	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2922076	1.00[YRI][hapmap]
rs3019295	1.00[JPT][hapmap]
rs34211616	0.84[EUR][1000 genomes]
rs34836224	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35018432	0.84[EUR][1000 genomes]
rs4131359	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4132545	0.95[JPT][hapmap]
rs4236854	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4260868	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4317539	0.84[EUR][1000 genomes]
rs4319053	0.84[EUR][1000 genomes]
rs4327836	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4374957	0.95[JPT][hapmap]
rs4380901	0.95[JPT][hapmap]
rs4394363	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4461878	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4489303	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4510823	0.95[JPT][hapmap]
rs4520132	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4612311	0.95[JPT][hapmap]
rs4734419	0.95[JPT][hapmap]
rs4734420	0.95[JPT][hapmap]
rs4734421	0.82[ASN][1000 genomes]
rs4735589	0.95[JPT][hapmap]
rs4735592	0.95[JPT][hapmap]
rs4735603	0.84[EUR][1000 genomes]
rs4735604	0.81[EUR][1000 genomes]
rs5019794	0.95[JPT][hapmap]
rs55691643	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55837765	0.83[EUR][1000 genomes]
rs55871624	0.84[EUR][1000 genomes]
rs56315283	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60950457	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60967421	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6415433	0.84[EUR][1000 genomes]
rs6468647	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6468663	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs6468664	0.95[JPT][hapmap]
rs6468665	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs6468669	0.84[EUR][1000 genomes]
rs6468671	0.83[EUR][1000 genomes]
rs6651157	0.95[JPT][hapmap]
rs6989201	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs6991283	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs6992480	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6993878	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6999263	0.86[JPT][hapmap]
rs7006391	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7011648	0.84[EUR][1000 genomes]
rs7012513	0.95[JPT][hapmap]
rs72668476	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668483	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72670294	0.83[EUR][1000 genomes]
rs72670297	0.84[EUR][1000 genomes]
rs72670301	0.84[EUR][1000 genomes]
rs72672309	0.84[EUR][1000 genomes]
rs72672313	0.84[EUR][1000 genomes]
rs7341605	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7460376	0.84[EUR][1000 genomes]
rs7461615	0.95[JPT][hapmap]
rs7462457	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7818037	0.95[JPT][hapmap]
rs7818051	0.83[EUR][1000 genomes]
rs7824113	0.95[JPT][hapmap]
rs7835084	0.84[EUR][1000 genomes]
rs7836899	0.84[EUR][1000 genomes]
rs7842393	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1023227	chr8:99902615-100290948	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv539692	chr8:99902615-100290948	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv6327	chr8:99919634-99964563	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv1803951	chr8:99922754-100191783	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv611809	chr8:99925628-100093510	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3019296	ARHGEF12	trans	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99925800-99935800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr8:99927200-99942000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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