Variant report

Variant	rs9829790
Chromosome Location	chr3:158105069-158105070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10049160	1.00[EUR][1000 genomes]
rs12330339	1.00[EUR][1000 genomes]
rs13317509	0.95[AFR][1000 genomes]
rs13321065	1.00[EUR][1000 genomes]
rs13322986	1.00[EUR][1000 genomes]
rs13323462	1.00[EUR][1000 genomes]
rs16829007	0.81[MKK][hapmap];1.00[EUR][1000 genomes]
rs28396261	1.00[EUR][1000 genomes]
rs28402668	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28428827	1.00[EUR][1000 genomes]
rs28506940	1.00[EUR][1000 genomes]
rs28608522	1.00[EUR][1000 genomes]
rs28646251	1.00[EUR][1000 genomes]
rs28680366	1.00[EUR][1000 genomes]
rs28720767	1.00[EUR][1000 genomes]
rs57550995	1.00[AMR][1000 genomes]
rs6441190	1.00[ASW][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441192	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762087	1.00[EUR][1000 genomes]
rs6762923	1.00[EUR][1000 genomes]
rs6765159	1.00[EUR][1000 genomes]
rs6767072	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775960	1.00[EUR][1000 genomes]
rs6776674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6784612	1.00[EUR][1000 genomes]
rs6784707	0.80[ASW][hapmap];0.84[MKK][hapmap];1.00[EUR][1000 genomes]
rs6786770	1.00[EUR][1000 genomes]
rs6786849	1.00[AMR][1000 genomes]
rs6787212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789607	0.83[MKK][hapmap];1.00[EUR][1000 genomes]
rs6790259	0.92[AFR][1000 genomes]
rs6798405	1.00[EUR][1000 genomes]
rs6801076	1.00[EUR][1000 genomes]
rs6804113	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs6807211	1.00[AMR][1000 genomes]
rs6810324	1.00[EUR][1000 genomes]
rs73013336	1.00[EUR][1000 genomes]
rs73017444	1.00[AMR][1000 genomes]
rs73017454	1.00[AMR][1000 genomes]
rs73017464	1.00[AMR][1000 genomes]
rs73017470	1.00[AMR][1000 genomes]
rs73017472	1.00[EUR][1000 genomes]
rs73027918	1.00[EUR][1000 genomes]
rs73028000	1.00[EUR][1000 genomes]
rs73028775	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73028779	1.00[EUR][1000 genomes]
rs73028802	1.00[AMR][1000 genomes]
rs73029897	1.00[EUR][1000 genomes]
rs73029899	1.00[EUR][1000 genomes]
rs73030514	1.00[EUR][1000 genomes]
rs73031618	1.00[EUR][1000 genomes]
rs73031643	1.00[EUR][1000 genomes]
rs73031646	1.00[EUR][1000 genomes]
rs7613737	1.00[EUR][1000 genomes]
rs7618252	1.00[EUR][1000 genomes]
rs7621282	1.00[EUR][1000 genomes]
rs7622013	0.80[ASW][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs7627082	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7633366	0.86[ASW][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs7635356	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638647	1.00[EUR][1000 genomes]
rs827133	0.81[AFR][1000 genomes]
rs9817119	1.00[EUR][1000 genomes]
rs9821945	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9824822	1.00[EUR][1000 genomes]
rs9838425	1.00[EUR][1000 genomes]
rs9841653	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs9843252	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846272	1.00[EUR][1000 genomes]
rs9852177	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs9852974	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs9861869	1.00[EUR][1000 genomes]
rs9863618	1.00[EUR][1000 genomes]
rs9868975	1.00[EUR][1000 genomes]
rs9869501	1.00[EUR][1000 genomes]
rs9870885	1.00[EUR][1000 genomes]
rs9872642	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9873074	1.00[EUR][1000 genomes]
rs9877427	1.00[EUR][1000 genomes]
rs9877843	1.00[EUR][1000 genomes]
rs9877873	1.00[EUR][1000 genomes]
rs9878828	1.00[EUR][1000 genomes]
rs9882507	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1000904	chr3:158094357-158159317	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1004480	chr3:158102068-158129826	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv536776	chr3:158102068-158129826	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9829790	RSRC1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158100800-158113200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:158104800-158105800	Enhancers	Fetal Heart	heart

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