Variant report

Variant	rs676034
Chromosome Location	chr3:52480446-52480447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr3:52480075-52481683	SK-N-SH	brain:	n/a	chr3:52481215-52481229 chr3:52481577-52481591 chr3:52481579-52481593 chr3:52481579-52481586
2	CTCF	chr3:52480360-52480650	HEK293	kidney:	n/a	chr3:52480505-52480518
3	CTCF	chr3:52480340-52480490	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52456149..52459336-chr3:52479539..52482914,3	MCF-7	breast:
2	chr3:52324567..52326107-chr3:52479756..52482200,2	K562	blood:
3	chr3:52479566..52481452-chr3:52488469..52490137,2	K562	blood:
4	chr3:52445252..52447300-chr3:52479403..52482047,3	MCF-7	breast:
5	chr3:52443376..52445165-chr3:52479554..52482269,2	K562	blood:

Variant related genes	Relation type
SEMA3G	TF binding region
ENSG00000163930	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1011062	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035002	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1035003	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077142	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10865972	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11707864	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs123598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs13065677	0.91[AMR][1000 genomes]
rs13071708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs13074649	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075370	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs13076890	1.00[JPT][hapmap]
rs13089892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13091360	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13091545	1.00[JPT][hapmap]
rs13093555	0.86[AMR][1000 genomes]
rs13096571	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13098856	0.91[AMR][1000 genomes]
rs1541495	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs164636	0.86[AMR][1000 genomes]
rs164637	0.86[AMR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2109558	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2109559	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335640	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2335928	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335929	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34181173	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34332947	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34385735	0.86[AMR][1000 genomes]
rs34551211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs34628357	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34762015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34827613	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35130772	0.91[AMR][1000 genomes]
rs352144	0.80[AMR][1000 genomes]
rs353545	0.86[AMR][1000 genomes]
rs35860312	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs35982798	0.81[AMR][1000 genomes]
rs3755810	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796342	0.91[AMR][1000 genomes]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419050	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs419604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs419752	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4312651	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	0.83[EUR][1000 genomes]
rs4687544	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687614	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687616	0.88[EUR][1000 genomes]
rs4687617	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4687618	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs575476	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61734640	0.81[AMR][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6414568	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445483	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445484	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445485	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6763882	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6787493	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795333	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297391	0.81[AMR][1000 genomes]
rs71297394	0.81[AMR][1000 genomes]
rs71297395	0.81[AMR][1000 genomes]
rs71297396	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs728408	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs758800	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs758803	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850471	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52470800-52484200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52477800-52480800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:52478200-52484000	Enhancers	Fetal Heart	heart
4	chr3:52478400-52481000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:52478600-52480600	Weak transcription	Right Atrium	heart
6	chr3:52478800-52480600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:52478800-52487600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:52479000-52480600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:52479000-52480600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:52479000-52480800	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:52479000-52481200	Enhancers	Lung	lung
12	chr3:52479200-52481200	Enhancers	Right Ventricle	heart
13	chr3:52479200-52481800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr3:52479200-52483800	Weak transcription	HMEC	breast
15	chr3:52479400-52480600	Weak transcription	Left Ventricle	heart
16	chr3:52479400-52480600	Weak transcription	HUVEC	blood vessel
17	chr3:52479400-52480800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:52479400-52480800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:52479400-52480800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:52479400-52480800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:52479400-52480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:52479400-52480800	Weak transcription	Brain Anterior Caudate	brain
23	chr3:52479400-52480800	Weak transcription	Fetal Thymus	thymus
24	chr3:52479400-52481000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:52479400-52481000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:52479400-52481000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:52479400-52481600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:52479400-52483000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:52479400-52483000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:52479400-52483800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:52479400-52483800	Weak transcription	Liver	Liver
32	chr3:52479400-52483800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:52479400-52483800	Weak transcription	A549	lung
34	chr3:52479400-52484000	Weak transcription	Esophagus	oesophagus
35	chr3:52479400-52484000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:52479400-52484200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:52479400-52484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:52479400-52485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:52479400-52487200	Weak transcription	GM12878-XiMat	blood
40	chr3:52479400-52488200	Weak transcription	Colonic Mucosa	Colon
41	chr3:52479600-52480600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:52479600-52480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:52479600-52480800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:52479600-52480800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:52479600-52480800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:52479600-52480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:52479600-52480800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:52479600-52481000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:52479600-52481000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:52479600-52481000	Weak transcription	Stomach Mucosa	stomach

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