Variant report

Variant	rs57519456
Chromosome Location	chr3:158095522-158095523
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158093335..158095765-chr3:158098415..158100643,2	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10936129	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1095642	0.94[ASN][1000 genomes]
rs1101158	0.81[ASN][1000 genomes]
rs11717725	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719188	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1193505	0.81[ASN][1000 genomes]
rs1193506	0.81[ASN][1000 genomes]
rs1193507	0.81[ASN][1000 genomes]
rs1193508	0.82[ASN][1000 genomes]
rs1193509	0.82[ASN][1000 genomes]
rs1193510	0.83[ASN][1000 genomes]
rs1193521	0.81[ASN][1000 genomes]
rs12107103	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12107104	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1212739	0.82[ASN][1000 genomes]
rs1213048	0.81[ASN][1000 genomes]
rs12494098	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496767	0.82[EUR][1000 genomes]
rs12629125	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12629587	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12632998	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633594	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12638169	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13066362	0.81[ASN][1000 genomes]
rs1526191	0.81[ASN][1000 genomes]
rs1526193	0.81[ASN][1000 genomes]
rs1526194	0.81[ASN][1000 genomes]
rs1618381	0.82[ASN][1000 genomes]
rs1630304	0.81[ASN][1000 genomes]
rs1724704	0.82[ASN][1000 genomes]
rs1730007	0.81[ASN][1000 genomes]
rs1730020	0.81[ASN][1000 genomes]
rs1730040	0.82[ASN][1000 genomes]
rs1730042	0.81[ASN][1000 genomes]
rs1730045	0.81[ASN][1000 genomes]
rs1852285	0.81[ASN][1000 genomes]
rs1983469	0.82[ASN][1000 genomes]
rs2176893	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2222326	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2362965	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2362968	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2362970	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682404	0.81[ASN][1000 genomes]
rs2682405	0.81[ASN][1000 genomes]
rs2682406	0.82[ASN][1000 genomes]
rs2693527	0.81[ASN][1000 genomes]
rs2693542	0.82[ASN][1000 genomes]
rs2698322	0.81[ASN][1000 genomes]
rs28578723	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28813180	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3845981	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4289388	0.94[EUR][1000 genomes]
rs4309677	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679828	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680426	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680431	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680433	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4680434	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4680436	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4680437	0.94[EUR][1000 genomes]
rs56387731	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60336101	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6414388	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6414390	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441188	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441195	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6441197	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441198	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6441201	0.82[EUR][1000 genomes]
rs67385174	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6767008	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6772237	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6772340	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6773939	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67761009	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785063	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788703	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6797629	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6800887	0.94[EUR][1000 genomes]
rs6806702	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73170315	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170348	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7426603	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7610691	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7610713	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7614259	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7621674	0.81[ASN][1000 genomes]
rs7621971	0.81[ASN][1000 genomes]
rs7632059	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7639867	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641954	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7643792	0.81[ASN][1000 genomes]
rs7648196	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827096	0.81[ASN][1000 genomes]
rs827097	0.81[ASN][1000 genomes]
rs827099	0.81[ASN][1000 genomes]
rs827101	0.81[ASN][1000 genomes]
rs827106	0.95[ASN][1000 genomes]
rs827126	0.81[ASN][1000 genomes]
rs827129	0.81[ASN][1000 genomes]
rs827131	0.81[ASN][1000 genomes]
rs827132	0.81[ASN][1000 genomes]
rs827134	0.94[ASN][1000 genomes]
rs827135	0.94[ASN][1000 genomes]
rs827137	0.81[ASN][1000 genomes]
rs827140	0.81[ASN][1000 genomes]
rs827163	0.81[ASN][1000 genomes]
rs827164	0.81[ASN][1000 genomes]
rs827166	0.81[ASN][1000 genomes]
rs827184	0.91[ASN][1000 genomes]
rs844119	0.81[ASN][1000 genomes]
rs864332	0.81[ASN][1000 genomes]
rs9784311	0.82[ASN][1000 genomes]
rs9809952	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9810345	0.85[EUR][1000 genomes]
rs9820370	0.81[ASN][1000 genomes]
rs9823076	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9827781	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843089	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9847045	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9847316	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9847460	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9850856	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9867152	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867617	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9870802	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9872089	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872889	0.82[EUR][1000 genomes]
rs9879545	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881630	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs57519456	RSRC1	cis	Esophagus Muscularis	GTEx
rs57519456	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158095400-158096400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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