Variant report

Variant	rs11731571
Chromosome Location	chr4:120221185-120221186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:120132610..120134570-chr4:120221091..120222996,2	MCF-7	breast:
2	chr4:120218971..120221940-chr4:120223972..120225739,2	MCF-7	breast:
3	chr4:120132319..120136069-chr4:120219720..120222326,6	MCF-7	breast:
4	chr4:120132453..120136158-chr4:120220202..120223113,6	K562	blood:
5	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
6	chr4:120220396..120223311-chr4:120987092..120990068,3	K562	blood:
7	chr4:120219760..120221715-chr4:120374891..120376939,2	MCF-7	breast:
8	chr4:120210891..120213027-chr4:120219123..120221721,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164096	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000245958	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000250938	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10003567	0.82[CHB][hapmap]
rs10006259	0.82[CHB][hapmap]
rs10006525	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs10006706	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs10006877	0.82[CHB][hapmap]
rs10017335	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs10029750	0.81[ASN][1000 genomes]
rs10032299	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1011054	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10518300	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs10518328	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs1052633	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11098496	0.80[ASN][1000 genomes]
rs11098497	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098498	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098499	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11098501	0.82[CHB][hapmap]
rs11724758	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11726229	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11729521	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs11732621	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732686	0.88[CHB][hapmap]
rs11734241	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs11737400	0.83[EUR][1000 genomes]
rs11935596	0.82[CHB][hapmap]
rs11944880	0.95[CHD][hapmap];0.86[JPT][hapmap]
rs12186259	0.86[JPT][hapmap]
rs12506395	0.81[ASN][1000 genomes]
rs12507565	0.82[CHB][hapmap]
rs12507964	0.82[CHB][hapmap]
rs12508504	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs12511640	0.82[CHB][hapmap]
rs12513083	0.82[CHB][hapmap]
rs12711071	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs13113112	0.95[CHD][hapmap];0.86[JPT][hapmap]
rs13113885	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116504	0.81[ASN][1000 genomes]
rs13129661	0.86[JPT][hapmap]
rs13133044	0.81[ASN][1000 genomes]
rs13149954	0.83[EUR][1000 genomes]
rs13435802	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1480931	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs1511015	0.80[ASN][1000 genomes]
rs1511017	0.82[CHB][hapmap]
rs1511018	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs1511019	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs1511025	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs1546502	0.82[CHB][hapmap]
rs1546503	0.82[CHB][hapmap]
rs1546505	0.82[CHB][hapmap];0.98[CHD][hapmap]
rs17006190	0.82[CHB][hapmap]
rs1980025	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs1980026	0.82[CHB][hapmap]
rs2036858	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2175383	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389803	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs2389809	0.82[CHB][hapmap]
rs28374891	0.81[ASN][1000 genomes]
rs28419773	0.81[ASN][1000 genomes]
rs28555550	0.81[ASN][1000 genomes]
rs28580295	0.82[EUR][1000 genomes]
rs2892848	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs35197422	0.80[ASN][1000 genomes]
rs35434465	0.80[ASN][1000 genomes]
rs35643470	0.81[ASN][1000 genomes]
rs3749591	0.82[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs62320740	0.83[EUR][1000 genomes]
rs6814412	0.80[ASN][1000 genomes]
rs6822808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6834796	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs6837898	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6843509	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847248	0.81[ASN][1000 genomes]
rs6848389	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs6849171	0.82[CHB][hapmap]
rs6849561	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs6849889	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6857105	0.81[ASN][1000 genomes]
rs714899	0.81[CHB][hapmap]
rs7659194	0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7659403	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7659501	0.82[CHB][hapmap]
rs7672594	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs7681544	0.82[CHB][hapmap]
rs7685268	0.81[JPT][hapmap]
rs878372	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs907205	0.82[CHB][hapmap]
rs9985932	0.86[YRI][hapmap]
rs9991959	0.82[CHB][hapmap];0.95[CHD][hapmap]
rs9998585	0.82[CHB][hapmap]
rs9999724	0.95[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11731571	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs11731571	TRPC3	cis	parietal	SCAN
rs11731571	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs11731571	USP53	cis	parietal	SCAN
rs11731571	BBS7	cis	parietal	SCAN
rs11731571	C4orf3	cis	Whole Blood	GTEx
rs11731571	BBS7	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120219200-120221600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:120219200-120222200	Active TSS	Aorta	Aorta
3	chr4:120219200-120222200	Active TSS	Right Ventricle	heart
4	chr4:120219200-120222400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:120219400-120222000	Active TSS	HMEC	breast
6	chr4:120219400-120222000	Active TSS	HSMMtube	muscle
7	chr4:120219400-120222200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:120219400-120222200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:120219400-120222400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:120219400-120222400	Active TSS	Fetal Intestine Large	intestine
11	chr4:120219400-120222400	Active TSS	NHLF	lung
12	chr4:120219600-120222400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr4:120219800-120221200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr4:120219800-120221800	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr4:120219800-120222000	Active TSS	Muscle Satellite Cultured Cells	--
16	chr4:120219800-120222400	Active TSS	HSMM	muscle
17	chr4:120220000-120221200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr4:120220000-120221200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr4:120220000-120221800	Active TSS	Placenta Amnion	Placenta Amnion
20	chr4:120220000-120222000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:120220000-120222000	Active TSS	Left Ventricle	heart
22	chr4:120220000-120222000	Active TSS	NHDF-Ad	bronchial
23	chr4:120220000-120222200	Active TSS	Fetal Muscle Trunk	muscle
24	chr4:120220000-120222200	Active TSS	Ovary	ovary
25	chr4:120220000-120222400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr4:120220000-120222400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr4:120220000-120222400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr4:120220000-120222400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:120220000-120222400	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr4:120220000-120222400	Active TSS	Fetal Kidney	kidney
31	chr4:120220000-120222400	Active TSS	A549	lung
32	chr4:120220000-120222400	Active TSS	Hela-S3	cervix
33	chr4:120220000-120223200	Active TSS	GM12878-XiMat	blood
34	chr4:120220200-120221200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr4:120220200-120221200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr4:120220200-120221200	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr4:120220200-120221400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr4:120220200-120221400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr4:120220200-120221600	Bivalent/Poised TSS	HepG2	liver
40	chr4:120220200-120221800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr4:120220200-120222200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:120220200-120222200	Active TSS	Esophagus	oesophagus
43	chr4:120220200-120222200	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr4:120220200-120222400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr4:120220400-120221200	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr4:120220400-120222000	Active TSS	Gastric	stomach
47	chr4:120220400-120222000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr4:120220400-120222200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:120220400-120222200	Active TSS	Lung	lung
50	chr4:120220400-120222400	Active TSS	H1 Cell Line	embryonic stem cell

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