Variant report

Variant	rs6778708
Chromosome Location	chr3:88243996-88243997
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	chr3:88241654..88244858-chr3:88247578..88250995,3	MCF-7	breast:

Extended variants
information (count: 177 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:176)

rs_ID	r²[population]
rs1006895	1.00[CEU][hapmap]
rs1006896	1.00[JPT][hapmap]
rs1051413	1.00[CEU][hapmap]
rs1051436	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs1063597	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs1063603	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs11128021	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12631689	0.97[EUR][1000 genomes]
rs12714702	0.95[EUR][1000 genomes]
rs13060704	0.97[EUR][1000 genomes]
rs13063511	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs13067183	0.99[EUR][1000 genomes]
rs13067419	0.83[EUR][1000 genomes]
rs13076170	0.94[CEU][hapmap]
rs13098157	0.87[CEU][hapmap]
rs13317261	0.97[EUR][1000 genomes]
rs2049817	0.94[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap]
rs2116149	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs2735556	1.00[JPT][hapmap]
rs2735559	1.00[JPT][hapmap]
rs28672845	0.93[EUR][1000 genomes]
rs28694532	0.96[EUR][1000 genomes]
rs3732776	1.00[CEU][hapmap]
rs3890707	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4241551	0.83[EUR][1000 genomes]
rs4257571	0.84[EUR][1000 genomes]
rs4276211	0.80[EUR][1000 genomes]
rs4276212	0.80[EUR][1000 genomes]
rs4337654	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs4368523	1.00[CEU][hapmap]
rs4374552	0.84[EUR][1000 genomes]
rs4384978	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4414876	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4429658	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4432672	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4434168	0.83[EUR][1000 genomes]
rs4438681	1.00[CEU][hapmap]
rs4485742	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4488864	0.84[EUR][1000 genomes]
rs4501136	0.84[EUR][1000 genomes]
rs4507280	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4518156	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4555548	0.84[EUR][1000 genomes]
rs4580585	0.84[EUR][1000 genomes]
rs4596173	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs4611846	1.00[CEU][hapmap]
rs4616670	0.82[EUR][1000 genomes]
rs4858931	1.00[CEU][hapmap]
rs4858935	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858936	0.90[EUR][1000 genomes]
rs4858937	0.97[EUR][1000 genomes]
rs4858938	0.99[EUR][1000 genomes]
rs4858981	1.00[CEU][hapmap]
rs4858983	0.85[CEU][hapmap]
rs4858985	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs4858994	1.00[CEU][hapmap]
rs4858995	0.83[EUR][1000 genomes]
rs4858998	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4858999	1.00[CEU][hapmap]
rs4859001	0.90[EUR][1000 genomes]
rs4859002	0.97[EUR][1000 genomes]
rs4859004	0.99[EUR][1000 genomes]
rs4859005	0.99[EUR][1000 genomes]
rs55744603	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55923163	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55936434	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60377014	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419867	0.80[EUR][1000 genomes]
rs6551271	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6551272	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6551273	0.81[EUR][1000 genomes]
rs6551274	0.84[EUR][1000 genomes]
rs6551275	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6551277	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6551278	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6551280	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6551281	1.00[JPT][hapmap]
rs6551282	0.88[EUR][1000 genomes]
rs6551283	0.89[EUR][1000 genomes]
rs6551284	0.90[EUR][1000 genomes]
rs6551285	0.90[EUR][1000 genomes]
rs6551286	0.90[EUR][1000 genomes]
rs6551288	0.90[EUR][1000 genomes]
rs6551289	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6551291	0.92[EUR][1000 genomes]
rs6551292	0.99[EUR][1000 genomes]
rs6551293	0.99[EUR][1000 genomes]
rs6551294	0.99[EUR][1000 genomes]
rs6551296	0.96[EUR][1000 genomes]
rs6551297	0.95[EUR][1000 genomes]
rs6551298	0.96[EUR][1000 genomes]
rs6762453	0.94[EUR][1000 genomes]
rs6767258	0.81[EUR][1000 genomes]
rs6771031	0.99[EUR][1000 genomes]
rs6777019	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs6781333	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6782507	0.84[EUR][1000 genomes]
rs6785359	0.90[EUR][1000 genomes]
rs6785560	0.96[EUR][1000 genomes]
rs6786788	0.83[EUR][1000 genomes]
rs6787824	1.00[CEU][hapmap]
rs6791133	0.88[EUR][1000 genomes]
rs6792208	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6793783	0.83[EUR][1000 genomes]
rs6796355	0.80[EUR][1000 genomes]
rs6801046	0.99[EUR][1000 genomes]
rs6804818	0.83[EUR][1000 genomes]
rs6805957	0.99[EUR][1000 genomes]
rs71616896	0.80[EUR][1000 genomes]
rs73132515	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7427047	0.99[EUR][1000 genomes]
rs7427296	0.97[EUR][1000 genomes]
rs7427335	0.99[EUR][1000 genomes]
rs7427704	0.81[EUR][1000 genomes]
rs7428357	0.99[EUR][1000 genomes]
rs7429120	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7430158	0.88[EUR][1000 genomes]
rs7431074	0.98[EUR][1000 genomes]
rs7431968	1.00[JPT][hapmap]
rs7432509	0.99[EUR][1000 genomes]
rs7432838	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7433285	0.90[EUR][1000 genomes]
rs7615585	0.95[EUR][1000 genomes]
rs7617691	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7618080	0.84[EUR][1000 genomes]
rs7618472	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs7620830	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7626777	0.83[EUR][1000 genomes]
rs7628689	0.89[EUR][1000 genomes]
rs7630028	0.83[EUR][1000 genomes]
rs7630240	0.84[EUR][1000 genomes]
rs7632123	0.90[EUR][1000 genomes]
rs7635996	0.83[EUR][1000 genomes]
rs7639420	0.84[EUR][1000 genomes]
rs7641173	0.88[EUR][1000 genomes]
rs7650707	0.84[EUR][1000 genomes]
rs7651641	0.81[EUR][1000 genomes]
rs7651999	1.00[CEU][hapmap]
rs7652528	0.97[EUR][1000 genomes]
rs7653652	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9310066	1.00[CEU][hapmap]
rs9310067	1.00[CEU][hapmap]
rs9310072	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9310074	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs9310077	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs959049	1.00[CEU][hapmap]
rs959050	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs9809661	0.99[EUR][1000 genomes]
rs9813894	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9814057	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9826925	1.00[JPT][hapmap]
rs9831230	0.99[EUR][1000 genomes]
rs9834468	0.80[EUR][1000 genomes]
rs9834501	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs9841834	0.99[EUR][1000 genomes]
rs9843550	0.99[EUR][1000 genomes]
rs9845776	1.00[CEU][hapmap]
rs9847322	0.81[EUR][1000 genomes]
rs9847355	0.99[EUR][1000 genomes]
rs9848258	0.99[EUR][1000 genomes]
rs9849248	0.99[EUR][1000 genomes]
rs9849353	0.99[EUR][1000 genomes]
rs9854138	0.88[EUR][1000 genomes]
rs9856990	0.96[EUR][1000 genomes]
rs9861398	0.81[EUR][1000 genomes]
rs9865335	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs9865578	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9865703	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9865710	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9866843	0.99[EUR][1000 genomes]
rs9868310	0.97[EUR][1000 genomes]
rs9868977	0.99[EUR][1000 genomes]
rs9873182	0.95[EUR][1000 genomes]
rs9876807	0.99[EUR][1000 genomes]
rs9881255	1.00[CEU][hapmap];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6778708	CGGBP1	cis	multi-tissue	Pritchard
rs6778708	ZNF654	cis	lymphoblastoid	seeQTL
rs6778708	ZNF654	cis	multi-tissue	Pritchard
rs6778708	CGGBP1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88237600-88244000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:88240200-88245800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:88240400-88246000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:88241600-88246000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:88241800-88246200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:88242000-88246000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:88242800-88246200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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