Variant report

Variant	rs4680433
Chromosome Location	chr3:158136848-158136849
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	chr3:158130354..158133315-chr3:158135794..158137911,2	MCF-7	breast:
2	chr3:158136221..158139181-chr3:158142409..158144374,2	K562	blood:

Extended variants
information (count: 150 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10936129	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10936133	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10936134	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1095627	0.86[JPT][hapmap]
rs1095637	0.80[CEU][hapmap]
rs1095641	0.86[JPT][hapmap]
rs1095642	0.86[JPT][hapmap]
rs11709804	0.96[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs11714869	0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs11717725	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719188	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193506	0.86[JPT][hapmap]
rs1193509	0.86[JPT][hapmap]
rs1193510	0.86[JPT][hapmap]
rs1193521	0.86[JPT][hapmap]
rs1210359	0.85[JPT][hapmap]
rs12107103	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107104	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1213048	0.86[JPT][hapmap]
rs12494098	0.96[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12496767	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12629125	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629587	0.96[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631196	0.83[ASN][1000 genomes]
rs12632998	0.96[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12633594	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638169	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13066362	0.86[JPT][hapmap]
rs1369562	0.91[GIH][hapmap];0.81[JPT][hapmap];0.96[MKK][hapmap];0.80[TSI][hapmap]
rs1630304	0.86[JPT][hapmap]
rs1714518	0.81[MKK][hapmap]
rs1730007	0.82[JPT][hapmap]
rs1730020	0.86[JPT][hapmap]
rs1730040	0.86[JPT][hapmap]
rs1852285	0.86[JPT][hapmap]
rs1978781	0.91[GIH][hapmap];0.81[JPT][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs2176893	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2222326	0.96[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2362965	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2362968	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2362970	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362972	0.92[ASN][1000 genomes]
rs2682405	0.86[JPT][hapmap]
rs2682406	0.86[JPT][hapmap]
rs2693529	0.86[JPT][hapmap]
rs2693542	0.86[JPT][hapmap]
rs28578723	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28813180	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28820925	0.98[ASN][1000 genomes]
rs3845981	0.96[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4289388	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4309677	0.96[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4510417	0.90[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap]
rs4561872	0.86[ASN][1000 genomes]
rs4679828	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680426	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4680431	0.96[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4680434	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680436	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680437	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56387731	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57519456	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60336101	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6414388	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6414390	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441188	0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6441195	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441197	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441198	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441200	0.90[ASN][1000 genomes]
rs6441201	0.89[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67385174	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767008	0.96[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6772237	0.81[EUR][1000 genomes]
rs6772340	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6774461	0.86[JPT][hapmap]
rs67761009	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6778370	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6783284	0.86[GIH][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs6785063	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6787172	0.81[JPT][hapmap]
rs6788703	0.96[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6791431	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6797629	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6800887	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806702	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73170315	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73170348	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7426603	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430565	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7610691	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610713	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7614259	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7620927	0.94[MKK][hapmap]
rs7632059	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639867	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7641954	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643792	0.86[JPT][hapmap]
rs7648196	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7648618	0.94[MKK][hapmap]
rs827092	0.86[JPT][hapmap]
rs827093	0.86[JPT][hapmap]
rs827094	0.86[JPT][hapmap]
rs827099	0.86[JPT][hapmap]
rs827106	0.86[JPT][hapmap]
rs827108	0.86[JPT][hapmap]
rs827113	0.86[JPT][hapmap]
rs827127	0.86[JPT][hapmap]
rs827129	0.86[JPT][hapmap]
rs827131	0.86[JPT][hapmap]
rs827134	0.86[JPT][hapmap]
rs827135	0.82[JPT][hapmap]
rs827164	0.86[JPT][hapmap]
rs827171	0.86[JPT][hapmap]
rs827176	0.82[JPT][hapmap]
rs827177	0.82[JPT][hapmap]
rs827178	0.82[JPT][hapmap]
rs827179	0.84[JPT][hapmap]
rs864332	0.86[JPT][hapmap]
rs939114	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs939117	0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap]
rs9809952	0.96[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9810345	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9811217	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9823076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827781	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9843089	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847045	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847316	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9847460	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850856	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858318	0.94[MKK][hapmap]
rs9859129	0.94[MKK][hapmap]
rs9867152	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9867617	0.96[CEU][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870802	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]
rs9872089	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872889	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9876322	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs9877909	0.99[ASN][1000 genomes]
rs9879545	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880806	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs9881630	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9882274	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9883657	0.94[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4680433	LXN	cis	parietal	SCAN
rs4680433	RSRC1	cis	Esophagus Muscularis	GTEx
rs4680433	LXN	cis	cerebellum	SCAN
rs4680433	RSRC1	cis	cerebellum	SCAN
rs4680433	RARRES1	cis	cerebellum	SCAN
rs4680433	GFM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158124600-158146600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:158134400-158137800	Weak transcription	Esophagus	oesophagus
3	chr3:158136600-158137600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:158136600-158138800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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