Variant report

Variant	rs9311474
Chromosome Location	chr3:52338852-52338853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52330648..52332485-chr3:52338517..52342537,3	K562	blood:
2	chr3:52336627..52339541-chr3:52378479..52380909,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1060330	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1077142	0.95[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap]
rs11705963	0.84[AFR][1000 genomes]
rs11706108	0.84[AFR][1000 genomes]
rs11716487	0.81[LWK][hapmap]
rs11717383	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091545	0.95[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs13094687	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs164640	0.87[JPT][hapmap]
rs181274	0.86[JPT][hapmap]
rs187084	0.87[JPT][hapmap]
rs2272088	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2276834	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34228726	0.84[ASN][1000 genomes]
rs34569561	0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs352139	0.87[GIH][hapmap];0.87[JPT][hapmap]
rs352140	0.87[JPT][hapmap]
rs352162	0.87[JPT][hapmap]
rs352163	0.87[JPT][hapmap]
rs352165	0.87[JPT][hapmap]
rs352166	0.87[JPT][hapmap]
rs352167	0.80[GIH][hapmap];0.87[JPT][hapmap]
rs352168	0.87[JPT][hapmap]
rs352169	0.87[JPT][hapmap]
rs352170	0.87[JPT][hapmap]
rs353547	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs35860312	0.95[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs3844291	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3852063	0.90[ASN][1000 genomes]
rs3852064	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs411457	0.81[CHB][hapmap]
rs498946	0.93[LWK][hapmap];0.86[MKK][hapmap];0.87[YRI][hapmap]
rs57615517	0.83[ASN][1000 genomes]
rs59565798	0.84[ASN][1000 genomes]
rs610060	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6445358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs648514	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs66462821	0.82[AFR][1000 genomes]
rs6794675	0.84[AFR][1000 genomes]
rs730050	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs7614727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7618915	0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7622851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629072	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7643570	0.95[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9311474	RBM6	cis	parietal	SCAN
rs9311474	SEMA3G	cis	parietal	SCAN
rs9311474	WDR82	cis	Liver	GTEx
rs9311474	GNL3	cis	parietal	SCAN
rs9311474	DNAH1	cis	cerebellum	SCAN
rs9311474	NT5DC2	cis	lymphoblastoid	seeQTL
rs9311474	NDUFAF3	cis	parietal	SCAN
rs9311474	RBM6	cis	cerebellum	SCAN
rs9311474	GNL3	cis	cerebellum	SCAN
rs9311474	ITIH4	cis	parietal	SCAN
rs9311474	NEK4	cis	parietal	SCAN
rs9311474	NEK4	cis	cerebellum	SCAN
rs9311474	SEMA3G	cis	cerebellum	SCAN
rs9311474	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs9311474	CACNA2D3	cis	parietal	SCAN
rs9311474	SPCS1	cis	parietal	SCAN
rs9311474	PPM1M	cis	multi-tissue	Pritchard
rs9311474	ARMET	cis	multi-tissue	Pritchard
rs9311474	GLYCTK	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
2	chr3:52325600-52340400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
4	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:52327600-52344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:52328200-52340200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:52328600-52340000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:52328800-52340200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:52330200-52343400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:52330200-52343400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:52330200-52345400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:52331000-52343200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:52331200-52342800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:52333000-52340800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:52333000-52341200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
22	chr3:52333400-52339200	Weak transcription	Colonic Mucosa	Colon
23	chr3:52334000-52340800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:52334000-52351400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:52334200-52347400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:52334200-52349600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:52334400-52340800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:52334400-52344000	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:52334400-52347200	Weak transcription	Esophagus	oesophagus
30	chr3:52334600-52339200	Weak transcription	Gastric	stomach
31	chr3:52334600-52339800	Weak transcription	Spleen	Spleen
32	chr3:52334600-52341200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:52334600-52341200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:52334600-52341400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:52334600-52342200	Weak transcription	Liver	Liver
36	chr3:52334600-52348000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:52335000-52341000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:52335000-52347600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:52335200-52339000	Weak transcription	Right Ventricle	heart
40	chr3:52335200-52339200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:52335200-52343200	Weak transcription	Placenta	Placenta
42	chr3:52335200-52343600	Weak transcription	Lung	lung
43	chr3:52335200-52345000	Weak transcription	HSMMtube	muscle
44	chr3:52335200-52347200	Weak transcription	Left Ventricle	heart
45	chr3:52335200-52347400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:52335200-52347600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:52335400-52340800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52335400-52344000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:52335400-52345000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:52335400-52351400	Weak transcription	Placenta Amnion	Placenta Amnion

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