Variant report

Variant	rs11732621
Chromosome Location	chr4:120212883-120212884
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120131829..120135322-chr4:120211531..120215532,3	MCF-7	breast:
2	chr4:120132040..120133786-chr4:120212228..120215179,3	K562	blood:
3	chr4:120211034..120213301-chr4:120221895..120223399,2	MCF-7	breast:
4	chr4:119950606..119952990-chr4:120212099..120214133,2	K562	blood:
5	chr4:120133768..120135369-chr4:120212161..120214535,2	K562	blood:
6	chr4:120210891..120213027-chr4:120219123..120221721,2	K562	blood:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000164096	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10006525	0.91[CHD][hapmap]
rs10006706	0.91[CHD][hapmap]
rs10010696	0.83[ASN][1000 genomes]
rs10017335	0.91[CHD][hapmap]
rs10029750	0.85[ASN][1000 genomes]
rs10031033	0.82[CHB][hapmap]
rs10032299	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011054	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10213342	0.83[ASN][1000 genomes]
rs10518300	0.93[CHD][hapmap]
rs10518328	0.91[CHD][hapmap]
rs1052633	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098496	0.84[ASN][1000 genomes]
rs11098497	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098498	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098499	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11724758	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11726229	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11729897	0.83[ASN][1000 genomes]
rs11731571	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	0.82[CHB][hapmap]
rs11734519	0.83[ASN][1000 genomes]
rs11737400	0.82[EUR][1000 genomes]
rs11931312	0.82[ASN][1000 genomes]
rs11944880	0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12186259	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12499598	0.80[ASN][1000 genomes]
rs12501610	0.83[ASN][1000 genomes]
rs12506395	0.85[ASN][1000 genomes]
rs12508504	0.91[CHD][hapmap]
rs12512517	0.83[ASN][1000 genomes]
rs12711071	0.93[CHD][hapmap]
rs13113112	0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs13113885	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114751	0.83[ASN][1000 genomes]
rs13116504	0.85[ASN][1000 genomes]
rs13129661	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13133044	0.85[ASN][1000 genomes]
rs13149954	0.82[EUR][1000 genomes]
rs13435802	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1397608	0.82[ASN][1000 genomes]
rs1480931	0.91[CHD][hapmap]
rs1511015	0.84[ASN][1000 genomes]
rs1511018	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1511019	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1511025	0.93[CHD][hapmap]
rs1546505	0.95[CHD][hapmap]
rs1551	0.82[ASN][1000 genomes]
rs1980025	0.93[CHD][hapmap]
rs2036858	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2175383	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389803	0.91[CHD][hapmap]
rs28374891	0.85[ASN][1000 genomes]
rs28419773	0.84[ASN][1000 genomes]
rs28555550	0.85[ASN][1000 genomes]
rs28580295	0.81[EUR][1000 genomes]
rs2892848	0.91[CHD][hapmap]
rs34585914	0.83[ASN][1000 genomes]
rs34616304	0.83[ASN][1000 genomes]
rs34630083	0.83[ASN][1000 genomes]
rs35197422	0.84[ASN][1000 genomes]
rs35271032	0.83[ASN][1000 genomes]
rs35434465	0.84[ASN][1000 genomes]
rs35643470	0.85[ASN][1000 genomes]
rs35916640	0.83[ASN][1000 genomes]
rs3749591	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4145951	0.83[ASN][1000 genomes]
rs56386062	0.82[ASN][1000 genomes]
rs62320740	0.82[EUR][1000 genomes]
rs6814412	0.84[ASN][1000 genomes]
rs6815725	0.82[ASN][1000 genomes]
rs6822808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6837898	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6843509	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6848389	0.91[CHD][hapmap]
rs6849561	0.88[CHD][hapmap]
rs6849889	0.86[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7659194	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7659403	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672594	0.93[CHD][hapmap]
rs7684942	0.81[ASN][1000 genomes]
rs7685268	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs878372	0.93[CHD][hapmap]
rs9991959	0.93[CHD][hapmap]
rs9999724	0.93[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11732621	RP11-384K6.6	cis	Whole Blood	GTEx
rs11732621	BBS7	cis	cerebellum	SCAN
rs11732621	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs11732621	C4orf3	cis	Whole Blood	GTEx
rs11732621	BBS7	cis	parietal	SCAN
rs11732621	TRPC3	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
2	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:120177000-120213600	Weak transcription	Lung	lung
4	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
6	chr4:120177200-120213600	Weak transcription	Esophagus	oesophagus
7	chr4:120178200-120213400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:120178200-120213600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:120178200-120213800	Weak transcription	Primary B cells from cord blood	blood
10	chr4:120178600-120217600	Weak transcription	Fetal Stomach	stomach
11	chr4:120187000-120219200	Weak transcription	Right Ventricle	heart
12	chr4:120193000-120217600	Weak transcription	Psoas Muscle	Psoas
13	chr4:120193000-120219200	Weak transcription	Fetal Brain Male	brain
14	chr4:120193800-120213600	Weak transcription	Left Ventricle	heart
15	chr4:120194600-120213400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:120201200-120220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:120201200-120220200	Weak transcription	Gastric	stomach
18	chr4:120201400-120220200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:120201800-120213600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:120201800-120213800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:120202000-120213400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:120202000-120213600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:120202000-120220200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:120203000-120213600	Weak transcription	Primary T cells from cord blood	blood
25	chr4:120206400-120213200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:120206400-120213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:120206400-120213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:120206400-120213400	Weak transcription	Ovary	ovary
29	chr4:120206400-120217400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:120206400-120217600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:120206400-120217600	Weak transcription	Fetal Intestine Small	intestine
32	chr4:120206400-120218200	Weak transcription	Aorta	Aorta
33	chr4:120206400-120219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:120206400-120219600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:120206400-120219800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:120206400-120219800	Weak transcription	Brain Substantia Nigra	brain
37	chr4:120206400-120220000	Weak transcription	Colonic Mucosa	Colon
38	chr4:120206600-120213400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:120206600-120213600	Weak transcription	Brain Anterior Caudate	brain
40	chr4:120206600-120213600	Weak transcription	Fetal Intestine Large	intestine
41	chr4:120206600-120213800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:120206600-120216600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:120206600-120216800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:120206600-120217600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:120206600-120217600	Weak transcription	Small Intestine	intestine
46	chr4:120206600-120219200	Weak transcription	Hela-S3	cervix
47	chr4:120206600-120219600	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:120206600-120219800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:120206600-120220200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:120206800-120213400	Weak transcription	Duodenum Mucosa	Duodenum

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