Variant report

Variant	rs634382
Chromosome Location	chr3:52482851-52482852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52482733-52483071	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:52481489..52483902-chr3:52737684..52740024,2	MCF-7	breast:
2	chr3:52481830..52487806-chr3:52487911..52490298,8	K562	blood:
3	chr3:52456149..52459336-chr3:52479539..52482914,3	MCF-7	breast:
4	chr3:52445308..52446845-chr3:52482628..52484238,2	MCF-7	breast:
5	chr3:52476521..52480604-chr3:52481219..52484302,3	MCF-7	breast:
6	chr3:52462441..52466581-chr3:52481054..52483159,4	K562	blood:
7	chr3:52461011..52465347-chr3:52480548..52485332,5	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA3G	TF binding region
ENSG00000114854	Chromatin interaction
ENSG00000010319	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000114902	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs1011064	1.00[JPT][hapmap]
rs1077142	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10865972	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11705963	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11706108	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11707864	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11707931	1.00[JPT][hapmap]
rs11709658	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11711934	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs11714402	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11716017	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11718125	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap]
rs123602	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs123603	1.00[JPT][hapmap]
rs13059674	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	0.86[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs13091360	1.00[JPT][hapmap]
rs13091545	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1541495	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17052058	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs17052061	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs17052068	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2016575	0.80[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109558	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2109559	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2159607	0.80[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2215466	1.00[JPT][hapmap]
rs2335640	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs28481563	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34238085	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34261027	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34355561	0.80[EUR][1000 genomes]
rs34523877	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs35860312	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3752819	0.80[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs390802	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs409803	0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
rs4312651	1.00[JPT][hapmap]
rs4687614	1.00[JPT][hapmap]
rs4687617	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4687618	1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[JPT][hapmap]
rs498946	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55965068	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55997317	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57441156	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs613519	0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6445386	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs648514	0.82[YRI][hapmap]
rs66462821	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6771558	1.00[JPT][hapmap]
rs6784615	1.00[JPT][hapmap]
rs6794675	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6796333	0.80[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs6800707	0.80[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6810027	1.00[JPT][hapmap]
rs728408	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs758803	1.00[JPT][hapmap]
rs7620015	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7643570	0.81[ASW][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs82825	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887514	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs887515	0.80[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9844183	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs634382	DNAH1	cis	cerebellum	SCAN
rs634382	NT5DC2	cis	parietal	SCAN
rs634382	SEMA3G	cis	cerebellum	SCAN
rs634382	NDUFAF3	cis	cerebellum	SCAN
rs634382	LOC286359	trans	parietal	SCAN
rs634382	DNAH1	cis	parietal	SCAN

Chromatin state (count:55 , 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	chr3:52478200-52484000	Enhancers	Fetal Heart	heart
3	chr3:52478800-52487600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:52479200-52483800	Weak transcription	HMEC	breast
5	chr3:52479400-52483000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:52479400-52483000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:52479400-52483800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:52479400-52483800	Weak transcription	Liver	Liver
9	chr3:52479400-52483800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:52479400-52483800	Weak transcription	A549	lung
11	chr3:52479400-52484000	Weak transcription	Esophagus	oesophagus
12	chr3:52479400-52484000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:52479400-52484200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:52479400-52484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:52479400-52485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52479400-52487200	Weak transcription	GM12878-XiMat	blood
17	chr3:52479400-52488200	Weak transcription	Colonic Mucosa	Colon
18	chr3:52479600-52483800	Weak transcription	Gastric	stomach
19	chr3:52479600-52483800	Weak transcription	Pancreas	Pancrea
20	chr3:52479600-52483800	Weak transcription	Hela-S3	cervix
21	chr3:52479600-52484000	Weak transcription	Spleen	Spleen
22	chr3:52479600-52487000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:52479600-52487400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:52479600-52487600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:52479600-52487600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:52479600-52487800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:52479800-52483800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:52480800-52483000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:52481000-52483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52481000-52483800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:52481200-52483800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:52481200-52483800	Weak transcription	Right Ventricle	heart
33	chr3:52481200-52484200	Weak transcription	Left Ventricle	heart
34	chr3:52481200-52484200	Enhancers	HepG2	liver
35	chr3:52481200-52484600	Weak transcription	Right Atrium	heart
36	chr3:52481200-52487600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:52481200-52490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr3:52481400-52487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:52481400-52488200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:52481600-52483800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:52481600-52483800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:52481600-52483800	Weak transcription	Placenta	Placenta
43	chr3:52481600-52484000	Weak transcription	Stomach Mucosa	stomach
44	chr3:52481600-52484400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:52481600-52487000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:52481600-52487200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:52481800-52483800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:52482200-52483800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:52482600-52483800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:52482800-52483000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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