Variant report

Variant	rs9870802
Chromosome Location	chr3:158148169-158148170
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10936129	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10936133	0.93[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs10936134	0.93[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs10936146	0.81[CEU][hapmap]
rs1095627	0.87[JPT][hapmap]
rs1095641	0.87[JPT][hapmap]
rs1095642	0.87[JPT][hapmap]
rs11709804	0.93[CEU][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]
rs11714869	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs11717725	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719188	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193506	0.87[JPT][hapmap]
rs1193509	0.86[JPT][hapmap]
rs1193510	0.86[JPT][hapmap]
rs1193521	0.87[JPT][hapmap]
rs1210359	0.85[JPT][hapmap]
rs12107103	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107104	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1213048	0.86[JPT][hapmap]
rs12494098	0.93[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12496767	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12629125	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629587	0.93[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631196	0.83[ASN][1000 genomes]
rs12632998	0.93[CEU][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12633594	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638169	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13066362	0.86[JPT][hapmap]
rs1369562	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1630304	0.87[JPT][hapmap]
rs1730007	0.82[JPT][hapmap]
rs1730020	0.87[JPT][hapmap]
rs1730040	0.87[JPT][hapmap]
rs1852285	0.86[JPT][hapmap]
rs1978779	0.85[CEU][hapmap]
rs1978781	0.81[JPT][hapmap]
rs2176893	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2222326	0.93[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2362965	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2362968	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]
rs2362970	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362972	0.92[ASN][1000 genomes]
rs2682405	0.86[JPT][hapmap]
rs2682406	0.87[JPT][hapmap]
rs2693529	0.87[JPT][hapmap]
rs2693542	0.87[JPT][hapmap]
rs28578723	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28813180	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28820925	0.98[ASN][1000 genomes]
rs3845981	0.93[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4289388	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4309677	0.93[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4510417	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs4561872	0.86[ASN][1000 genomes]
rs4679828	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680426	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4680431	0.92[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4680433	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680434	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680437	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56387731	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57519456	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60336101	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6414388	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6414390	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441188	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6441195	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441197	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441198	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441200	0.90[ASN][1000 genomes]
rs6441201	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67385174	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767008	0.93[CEU][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6772340	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6774461	0.86[JPT][hapmap]
rs67761009	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6778202	0.82[CEU][hapmap]
rs6778370	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6783284	0.81[CEU][hapmap]
rs6785063	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6787172	0.82[JPT][hapmap]
rs6788703	0.93[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6791431	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6797629	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6800887	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806702	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73170315	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73170348	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7426603	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430565	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7610691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610713	0.92[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7614259	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7632059	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639867	0.89[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7641954	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643792	0.86[JPT][hapmap]
rs7648196	0.93[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs827092	0.87[JPT][hapmap]
rs827093	0.87[JPT][hapmap]
rs827094	0.87[JPT][hapmap]
rs827099	0.86[JPT][hapmap]
rs827106	0.86[JPT][hapmap]
rs827108	0.86[JPT][hapmap]
rs827113	0.86[JPT][hapmap]
rs827127	0.87[JPT][hapmap]
rs827129	0.86[JPT][hapmap]
rs827131	0.87[JPT][hapmap]
rs827134	0.87[JPT][hapmap]
rs827135	0.82[JPT][hapmap]
rs827164	0.87[JPT][hapmap]
rs827171	0.86[JPT][hapmap]
rs827176	0.83[JPT][hapmap]
rs827177	0.83[JPT][hapmap]
rs827178	0.82[JPT][hapmap]
rs827179	0.85[JPT][hapmap]
rs864332	0.86[JPT][hapmap]
rs939114	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs939117	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs9809952	0.93[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9810345	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9811217	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9823076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827781	0.92[CEU][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9835244	0.82[CEU][hapmap]
rs9843089	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847045	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847316	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847460	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850856	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867152	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9867617	0.92[CEU][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872089	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872889	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9876322	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9877909	0.99[ASN][1000 genomes]
rs9879545	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880806	0.93[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs9881630	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9882274	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916910	chr3:157926799-158183372	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1000904	chr3:158094357-158159317	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9870802	RSRC1	cis	Esophagus Muscularis	GTEx
rs9870802	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158145600-158164600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:158146000-158149800	Weak transcription	Fetal Intestine Large	intestine
3	chr3:158148000-158148400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:158148000-158149000	Enhancers	Placenta Amnion	Placenta Amnion

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