Variant report

Variant	rs1077142
Chromosome Location	chr3:52403526-52403527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52391704..52393563-chr3:52402367..52404938,2	MCF-7	breast:
2	chr3:52389433..52392179-chr3:52403246..52405082,2	K562	blood:
3	chr3:52399471..52401376-chr3:52402846..52405775,2	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs1060330	0.80[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11706001	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11706108	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707864	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11709658	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11711934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11714402	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716017	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11716487	0.86[LWK][hapmap]
rs11717383	0.91[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap]
rs11718125	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs123602	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs123603	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13059674	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13060192	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089892	1.00[CHD][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052061	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17052068	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016575	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs2215466	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2335640	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28481563	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34238085	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34261027	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34355561	0.92[EUR][1000 genomes]
rs34523877	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34908451	0.93[EUR][1000 genomes]
rs35133416	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752819	0.92[EUR][1000 genomes]
rs3755810	1.00[CHD][hapmap]
rs3774409	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs390802	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs409803	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs419050	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs419604	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs419752	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4312651	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687614	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687617	1.00[JPT][hapmap]
rs4687618	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs498946	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55965068	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55997317	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56357549	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57441156	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59612757	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs610060	0.80[LWK][hapmap];0.89[MKK][hapmap]
rs61150019	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs634382	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]
rs6445358	0.93[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap]
rs6445386	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67248391	0.93[EUR][1000 genomes]
rs676034	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6763882	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.93[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6794675	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6796333	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6800707	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6810027	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs728408	1.00[JPT][hapmap]
rs758803	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7614727	0.93[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap]
rs7620015	1.00[JPT][hapmap]
rs7622851	0.95[YRI][hapmap]
rs7643570	1.00[ASW][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs82825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9844183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9861879	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[CHD][hapmap];1.00[JPT][hapmap]

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	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
4	nsv979833	chr3:52387550-52407592	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1077142	DNAH1	cis	parietal	SCAN
rs1077142	SEMA3G	cis	cerebellum	SCAN
rs1077142	ITIH3	cis	parietal	SCAN
rs1077142	LOC286359	trans	parietal	SCAN
rs1077142	DNAH1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
2	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:52375400-52405600	Strong transcription	Lung	lung
4	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:52377000-52406600	Strong transcription	Liver	Liver
6	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
13	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:52381400-52404200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:52381400-52407400	Weak transcription	NHLF	lung
18	chr3:52381600-52405400	Strong transcription	Adipose Nuclei	Adipose
19	chr3:52381600-52405800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:52384600-52406200	Weak transcription	GM12878-XiMat	blood
21	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
22	chr3:52386000-52406600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:52390400-52405600	Weak transcription	Fetal Brain Female	brain
24	chr3:52392200-52406400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:52392600-52406600	Strong transcription	Primary T cells from cord blood	blood
26	chr3:52393000-52406400	Strong transcription	Thymus	Thymus
27	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:52393600-52404600	Strong transcription	Primary B cells from cord blood	blood
29	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
30	chr3:52395200-52407200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:52395400-52409400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
33	chr3:52396000-52404200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:52397400-52407400	Weak transcription	Fetal Lung	lung
35	chr3:52397600-52403800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:52398000-52407400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
39	chr3:52399000-52409400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:52399400-52409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:52399600-52403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:52399600-52404800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:52399800-52403800	Enhancers	Brain Substantia Nigra	brain
44	chr3:52400000-52403600	Genic enhancers	Brain Angular Gyrus	brain
45	chr3:52400200-52409200	Weak transcription	Right Ventricle	heart
46	chr3:52401000-52409400	Weak transcription	Esophagus	oesophagus
47	chr3:52401200-52403800	Genic enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:52401200-52404000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:52401200-52404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:52401200-52409400	Weak transcription	Colonic Mucosa	Colon

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