Variant report

Variant	rs6796333
Chromosome Location	chr3:52359678-52359679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52355477..52357613-chr3:52358216..52360675,2	K562	blood:
2	chr3:52324226..52326075-chr3:52357786..52360514,2	K562	blood:
3	chr3:52321124..52323557-chr3:52359639..52361279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs10460962	0.83[ASW][hapmap];0.97[LWK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs10461028	0.89[AFR][1000 genomes]
rs1077142	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]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706001	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11706108	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11707864	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs11707931	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11709658	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11710014	0.89[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs11711934	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711974	0.84[LWK][hapmap]
rs11714402	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11716017	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11718125	0.87[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap]
rs123602	0.83[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs123603	1.00[JPT][hapmap]
rs13059674	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	0.83[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap]
rs13091545	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052053	0.83[ASW][hapmap];1.00[LWK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs17052054	0.83[ASW][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs17052058	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17052061	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052068	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2016575	0.87[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.87[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs2215466	1.00[JPT][hapmap]
rs2335640	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28481563	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34238085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34261027	0.80[EUR][1000 genomes]
rs34355561	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34523877	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34908451	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35133416	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	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]
rs3733063	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs3752819	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs390802	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4082828	0.81[LWK][hapmap]
rs409803	1.00[JPT][hapmap]
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	1.00[JPT][hapmap]
rs4687618	1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[JPT][hapmap]
rs498946	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55965068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55997317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56352611	0.93[AFR][1000 genomes]
rs56357549	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57441156	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59612757	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61150019	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap]
rs634382	0.80[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs6445385	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs6445386	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67248391	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6793317	0.83[LWK][hapmap]
rs6794675	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6800707	0.87[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6810027	1.00[JPT][hapmap]
rs728408	1.00[JPT][hapmap]
rs73088800	0.93[AFR][1000 genomes]
rs758803	1.00[JPT][hapmap]
rs7615405	0.88[AFR][1000 genomes]
rs7620015	1.00[JPT][hapmap]
rs7643570	0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs82825	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs929528	1.00[JPT][hapmap]
rs9844183	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
3	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	90 gene(s)	inside rSNPs	diseases
4	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6796333	ITIH3	cis	parietal	SCAN
rs6796333	DNAH1	cis	parietal	SCAN
rs6796333	SEMA3G	cis	cerebellum	SCAN
rs6796333	PPM1M	cis	parietal	SCAN
rs6796333	DNAH1	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
2	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52350600-52362400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:52352000-52360600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:52352000-52361400	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:52352000-52362200	Weak transcription	Thymus	Thymus
9	chr3:52352000-52365000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:52352000-52365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52352000-52365800	Weak transcription	Aorta	Aorta
12	chr3:52352000-52367600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:52352000-52379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:52352200-52362000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:52352200-52364800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:52352200-52370800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:52352200-52379000	Weak transcription	Colonic Mucosa	Colon
18	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:52352400-52360000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:52352400-52360800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:52352400-52361200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:52352400-52364600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:52352400-52364800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:52352400-52365200	Weak transcription	Placenta	Placenta
26	chr3:52352400-52366000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:52352400-52366000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:52352400-52366200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:52352600-52362000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:52352600-52362600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:52352600-52365400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:52352600-52373400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:52352600-52379400	Weak transcription	Pancreas	Pancrea
34	chr3:52352800-52365800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:52352800-52365800	Weak transcription	Gastric	stomach
36	chr3:52353200-52360200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:52353200-52364400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:52353400-52377400	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:52353800-52360200	Weak transcription	Fetal Stomach	stomach
40	chr3:52354400-52379800	Weak transcription	Esophagus	oesophagus
41	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:52357000-52366200	Weak transcription	Primary B cells from cord blood	blood
43	chr3:52357200-52365000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:52357400-52359800	Weak transcription	Spleen	Spleen
45	chr3:52357400-52360600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:52357400-52361600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:52357800-52361800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:52358000-52362400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:52358200-52362400	Weak transcription	Primary T cells from cord blood	blood
50	chr3:52358200-52372000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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