Variant report

Variant	rs6803519
Chromosome Location	chr3:52889771-52889772
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	chr3:52888069..52891024-chr3:53081330..53083131,2	K562	blood:
2	chr3:52888488..52890920-chr3:53078565..53080433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11130331	0.82[JPT][hapmap]
rs1134546	0.82[CEU][hapmap];0.88[TSI][hapmap]
rs11918800	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs11922961	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11922975	0.82[JPT][hapmap]
rs12492391	0.95[JPT][hapmap]
rs13072536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs13083728	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1573815	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs17304995	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs2071042	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2239547	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs2240915	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2256332	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2276815	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2276816	0.82[GIH][hapmap]
rs2276817	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2276825	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2336668	0.95[JPT][hapmap]
rs2336669	0.82[CEU][hapmap];0.85[GIH][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap]
rs2535633	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2564947	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs2581780	0.82[CEU][hapmap]
rs2581801	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs2581810	0.82[CEU][hapmap]
rs2581815	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs3733047	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap]
rs3821873	0.94[JPT][hapmap]
rs4302374	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4519686	0.82[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs4687554	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs4687657	0.91[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs4687658	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4687663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4687672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4687680	0.95[JPT][hapmap]
rs4687682	0.95[JPT][hapmap]
rs4687687	0.86[JPT][hapmap]
rs6445538	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs6445539	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6445541	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6445547	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6445550	0.82[CEU][hapmap];0.82[GIH][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap]
rs6768844	0.82[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs6769789	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6790314	0.89[YRI][hapmap]
rs6792578	0.82[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs6795646	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs7626551	0.86[JPT][hapmap]
rs7648514	0.82[CEU][hapmap]
rs9311485	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs9682464	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9810807	0.95[JPT][hapmap]
rs9836499	0.95[JPT][hapmap]
rs9844736	0.82[CEU][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs9846976	0.82[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs9850563	0.95[JPT][hapmap]
rs9860296	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs9865094	0.86[CEU][hapmap]
rs9876403	0.87[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs9880978	0.95[JPT][hapmap]
rs9985365	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs6803519	SEMA3G	cis	parietal	SCAN
rs6803519	TMEM110	cis	parietal	SCAN
rs6803519	ITIH4	cis	lymphoblastoid	seeQTL
rs6803519	NEK4	cis	parietal	SCAN
rs6803519	ITIH4	trans	brain	seeQTL
rs6803519	ITIH4	cis	cerebellum	SCAN
rs6803519	GLT8D1	cis	lymphoblastoid	seeQTL
rs6803519	AMT	cis	parietal	SCAN
rs6803519	ITIH4	cis	multi-tissue	Pritchard
rs6803519	ITIH4	cis	Lymphoblastoid	GTEx
rs6803519	ITIH4	cis	parietal	SCAN
rs6803519	GNL3	cis	parietal	SCAN
rs6803519	GNL3	cis	cerebellum	SCAN
rs6803519	RFT1	cis	cerebellum	SCAN
rs6803519	GLT8D1	trans	brain	seeQTL
rs6803519	GLT8D1	cis	brain	seeQTL
rs6803519	RBM6	cis	parietal	SCAN
rs6803519	ITIH4	cis	brain	seeQTL
rs6803519	TMEM110	cis	cerebellum	SCAN
rs6803519	PPM1M	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
2	chr3:52873400-52891600	Strong transcription	Primary T cells from cord blood	blood
3	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52873800-52891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:52879600-52889800	Weak transcription	K562	blood
6	chr3:52879800-52894800	Weak transcription	HSMM	muscle
7	chr3:52880200-52890200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:52880400-52890000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:52880600-52891000	Weak transcription	Fetal Heart	heart
10	chr3:52880800-52889800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:52880800-52890000	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:52881200-52890000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:52881200-52890200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:52881200-52890200	Strong transcription	Adipose Nuclei	Adipose
15	chr3:52881800-52890000	Strong transcription	Thymus	Thymus
16	chr3:52883200-52889800	Weak transcription	Osteobl	bone
17	chr3:52883400-52894200	Weak transcription	HSMMtube	muscle
18	chr3:52883400-52894600	Weak transcription	Hela-S3	cervix
19	chr3:52883800-52894400	Weak transcription	Psoas Muscle	Psoas
20	chr3:52884000-52898200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:52884200-52893000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:52884400-52893000	Weak transcription	Small Intestine	intestine
24	chr3:52885400-52890000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:52885400-52899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:52885600-52890000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:52886000-52891000	Strong transcription	Fetal Thymus	thymus
28	chr3:52886200-52907800	Weak transcription	NHLF	lung
29	chr3:52886400-52894200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:52886600-52890800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:52886600-52890800	Weak transcription	Pancreas	Pancrea
32	chr3:52886600-52890800	Weak transcription	Right Ventricle	heart
33	chr3:52886600-52891000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:52886600-52891200	Weak transcription	Spleen	Spleen
35	chr3:52886600-52891400	Weak transcription	Brain Substantia Nigra	brain
36	chr3:52886600-52891600	Weak transcription	Fetal Lung	lung
37	chr3:52886600-52894400	Weak transcription	Esophagus	oesophagus
38	chr3:52886600-52894400	Weak transcription	Gastric	stomach
39	chr3:52886600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:52886600-52894600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:52886600-52895000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:52886600-52897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:52886600-52897600	Weak transcription	Fetal Intestine Small	intestine
44	chr3:52886600-52897800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:52886600-52899800	Weak transcription	Dnd41	blood
47	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood

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