Variant report

Variant	rs6773939
Chromosome Location	chr3:158069706-158069707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158063983..158067425-chr3:158069212..158071955,3	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10936129	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1095642	0.87[ASN][1000 genomes]
rs11717725	0.81[EUR][1000 genomes]
rs11719188	0.83[EUR][1000 genomes]
rs12107103	0.82[EUR][1000 genomes]
rs12107104	0.82[EUR][1000 genomes]
rs12494098	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629125	0.82[EUR][1000 genomes]
rs12629587	0.83[EUR][1000 genomes]
rs12632998	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12633594	0.82[EUR][1000 genomes]
rs12638169	0.82[EUR][1000 genomes]
rs2176893	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2222326	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2362965	0.83[EUR][1000 genomes]
rs2362968	0.82[EUR][1000 genomes]
rs2362970	0.82[EUR][1000 genomes]
rs28578723	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28813180	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3845981	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4289388	0.81[EUR][1000 genomes]
rs4309677	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679828	0.82[EUR][1000 genomes]
rs4680426	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680431	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680434	0.81[EUR][1000 genomes]
rs4680436	0.81[EUR][1000 genomes]
rs4680437	0.80[EUR][1000 genomes]
rs56387731	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57519456	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60336101	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6414388	0.83[EUR][1000 genomes]
rs6414390	0.82[EUR][1000 genomes]
rs6441188	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441195	0.81[EUR][1000 genomes]
rs6441198	0.81[EUR][1000 genomes]
rs67385174	0.83[EUR][1000 genomes]
rs6767008	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6772340	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67761009	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6785063	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6788703	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6797629	0.83[ASN][1000 genomes]
rs6800887	0.81[EUR][1000 genomes]
rs6806702	0.81[EUR][1000 genomes]
rs73170315	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73170348	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7426603	0.83[EUR][1000 genomes]
rs7610691	0.81[EUR][1000 genomes]
rs7610713	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7614259	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7632059	0.82[EUR][1000 genomes]
rs7639867	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7641954	0.80[EUR][1000 genomes]
rs7648196	0.83[EUR][1000 genomes]
rs827106	0.86[ASN][1000 genomes]
rs827134	0.87[ASN][1000 genomes]
rs827135	0.87[ASN][1000 genomes]
rs827184	0.84[ASN][1000 genomes]
rs9809952	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9823076	0.81[EUR][1000 genomes]
rs9827781	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9847045	0.82[EUR][1000 genomes]
rs9847460	0.81[EUR][1000 genomes]
rs9850856	0.82[EUR][1000 genomes]
rs9867152	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9867617	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9872089	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9879545	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9881630	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6773939	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158047800-158077800	Weak transcription	Gastric	stomach
2	chr3:158048200-158079400	Weak transcription	Right Ventricle	heart
3	chr3:158055000-158077200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:158055200-158086000	Weak transcription	Left Ventricle	heart
5	chr3:158057800-158079600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:158060000-158069800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:158060000-158069800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:158068800-158077400	Weak transcription	Adipose Nuclei	Adipose
9	chr3:158069600-158071600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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