Variant report

Variant	rs486451
Chromosome Location	chr11:62493600-62493601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:60)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr11:62493074-62494016	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:62493469-62496686	SK-N-MC	brain:	n/a	n/a
3	ZKSCAN1	chr11:62493051-62496633	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr11:62492956-62496614	Hela-S3	cervix:	n/a	chr11:62495595-62495612 chr11:62495597-62495608 chr11:62493020-62493033
5	POLR2A	chr11:62493548-62494078	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:62493578-62496616	Hela-S3	cervix:	n/a	n/a
7	WRNIP1	chr11:62492919-62494195	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:62493551-62493606	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:62493234-62496631	HepG2	liver:	n/a	n/a
10	TCF12	chr11:62493518-62496682	A549	lung:	n/a	n/a
11	BRCA1	chr11:62492996-62494289	Hela-S3	cervix:	n/a	n/a
12	HCFC1	chr11:62491528-62497135	Hela-S3	cervix:	n/a	n/a
13	GTF3C2	chr11:62493093-62493853	Hela-S3	cervix:	n/a	n/a
14	USF2	chr11:62493066-62493892	Hela-S3	cervix:	n/a	n/a
15	CHD1	chr11:62493138-62496440	GM12878	blood:	n/a	n/a
16	REST	chr11:62493515-62496900	H1-neurons	neurons:	n/a	chr11:62494019-62494032 chr11:62494863-62494873 chr11:62494022-62494035 chr11:62495654-62495667
17	ZNF143	chr11:62493216-62496543	Hela-S3	cervix:	n/a	n/a
18	TBP	chr11:62493032-62493618	Hela-S3	cervix:	n/a	n/a
19	MXI1	chr11:62492150-62497591	SK-N-SH	brain:	n/a	n/a
20	SMC3	chr11:62493066-62496538	Hela-S3	cervix:	n/a	chr11:62495666-62495674 chr11:62494950-62494964
21	ZNF263	chr11:62493193-62495242	HEK293-T-REx	kidney:	n/a	chr11:62494383-62494404
22	MXI1	chr11:62493096-62496715	Hela-S3	cervix:	n/a	n/a
23	RFX5	chr11:62493084-62496788	Hela-S3	cervix:	n/a	n/a
24	MAX	chr11:62493102-62496642	Hela-S3	cervix:	n/a	chr11:62495135-62495145
25	MTA3	chr11:62493440-62494227	GM12878	blood:	n/a	n/a
26	POLR2A	chr11:62493454-62493828	SK-N-SH	brain:	n/a	n/a
27	HEY1	chr11:62493155-62493897	HepG2	liver:	n/a	n/a
28	CHD1	chr11:62492749-62496826	IMR90	lung:	n/a	n/a
29	TFAP2C	chr11:62492862-62496263	Hela-S3	cervix:	n/a	chr11:62493261-62493276
30	SIN3A	chr11:62493197-62496636	H1-hESC	embryonic stem cell:	n/a	chr11:62494019-62494030 chr11:62493317-62493325
31	POLR2A	chr11:62493551-62496637	GM12878	blood:	n/a	n/a
32	RCOR1	chr11:62493086-62496761	Hela-S3	cervix:	n/a	n/a
33	TFAP2A	chr11:62492920-62495445	Hela-S3	cervix:	n/a	chr11:62494960-62494972 chr11:62494961-62494972 chr11:62493261-62493275 chr11:62494961-62494972 chr11:62494963-62494971 chr11:62493261-62493275 chr11:62494963-62494971 chr11:62494963-62494971 chr11:62494961-62494972 chr11:62493261-62493275
34	MXI1	chr11:62492942-62496705	IMR90	lung:	n/a	n/a
35	SIN3AK20	chr11:62492927-62496653	MCF-7	breast:	n/a	n/a
36	POLR2A	chr11:62493137-62493857	HepG2	liver:	n/a	n/a
37	UBTF	chr11:62493554-62495302	K562	blood:	n/a	n/a
38	MAZ	chr11:62493105-62496578	Hela-S3	cervix:	n/a	chr11:62495135-62495145
39	POLR2A	chr11:62493117-62493625	MCF-7	breast:	n/a	n/a

No data

(count:60 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr11:62412098..62414534-chr11:62491927..62496781,5	K562	blood:
2	chr11:62363862..62365574-chr11:62493189..62495002,2	MCF-7	breast:
3	chr11:62491589..62497348-chr11:62553332..62556416,10	K562	blood:
4	chr11:62371312..62376313-chr11:62493293..62497173,4	MCF-7	breast:
5	chr11:62357079..62360474-chr11:62493562..62497187,4	MCF-7	breast:
6	chr11:62493487..62501439-chr11:62552997..62556820,17	MCF-7	breast:
7	chr11:62492351..62496994-chr11:62525479..62531629,8	MCF-7	breast:
8	chr11:62413530..62415536-chr11:62492438..62494728,3	MCF-7	breast:
9	chr11:62492872..62497892-chr11:62536194..62540986,8	K562	blood:
10	chr11:62429368..62441438-chr11:62488512..62498189,36	K562	blood:
11	chr11:62492410..62497148-chr11:62620379..62625675,11	K562	blood:
12	chr11:62430955..62435240-chr11:62493417..62497695,13	K562	blood:
13	chr11:62489679..62493629-chr11:62495825..62497896,4	K562	blood:
14	chr11:62445290..62447027-chr11:62493519..62496962,3	K562	blood:
15	chr11:62487366..62497836-chr11:62605953..62610629,27	K562	blood:
16	chr11:62492410..62497430-chr11:62621392..62625675,11	K562	blood:
17	chr11:62492343..62497215-chr11:62619514..62625025,15	MCF-7	breast:
18	chr11:62492533..62495700-chr11:62653873..62657613,5	K562	blood:
19	chr11:62493462..62498807-chr11:62519015..62523330,14	K562	blood:
20	chr11:62493399..62495711-chr11:62557116..62560214,4	K562	blood:
21	chr11:62412098..62414534-chr11:62492500..62497433,5	K562	blood:
22	chr11:62489834..62499984-chr11:62527523..62534733,19	MCF-7	breast:
23	chr11:62365667..62370630-chr11:62493549..62497299,5	MCF-7	breast:
24	chr11:62491904..62497981-chr11:62597734..62601812,7	MCF-7	breast:
25	chr11:62338750..62340905-chr11:62493319..62495398,2	MCF-7	breast:
26	chr11:62491838..62494453-chr11:62503322..62504872,2	MCF-7	breast:
27	chr11:62487017..62500577-chr11:62602457..62611761,54	MCF-7	breast:
28	chr11:62492964..62497505-chr11:62605703..62612812,19	K562	blood:
29	chr11:62492430..62497674-chr11:62536203..62540726,8	MCF-7	breast:
30	chr11:62431330..62441336-chr11:62489515..62497875,29	MCF-7	breast:
31	chr11:62431689..62434905-chr11:62493467..62497648,6	MCF-7	breast:
32	chr11:62437179..62441189-chr11:62491770..62496446,10	K562	blood:
33	chr11:62493351..62498967-chr11:62525383..62529651,6	K562	blood:
34	chr11:62493384..62497236-chr11:62520063..62523255,11	K562	blood:
35	chr11:62356516..62363396-chr11:62492172..62497480,8	K562	blood:
36	chr11:62444918..62447837-chr11:62491934..62496304,8	MCF-7	breast:
37	chr11:62367890..62370349-chr11:62493262..62495403,4	K562	blood:
38	chr11:62493028..62494809-chr11:62648361..62650333,2	K562	blood:
39	chr11:62491993..62498335-chr11:62552883..62557132,13	MCF-7	breast:
40	chr11:62339643..62341464-chr11:62493039..62495603,2	MCF-7	breast:
41	chr11:62492683..62497467-chr11:62646838..62651892,11	MCF-7	breast:
42	chr11:62491654..62494527-chr11:62557259..62560768,3	MCF-7	breast:
43	chr11:62490982..62494265-chr11:62506317..62509112,3	MCF-7	breast:
44	chr11:62377536..62380529-chr11:62493370..62497128,3	K562	blood:
45	chr11:62493159..62495020-chr11:62623607..62625320,2	MCF-7	breast:
46	chr11:62379764..62382350-chr11:62493558..62496251,2	MCF-7	breast:
47	chr11:62491539..62497784-chr11:62516835..62523459,19	MCF-7	breast:
48	chr11:62492996..62496945-chr11:62646247..62651278,7	K562	blood:
49	chr11:62492464..62497553-chr11:62519802..62523353,13	MCF-7	breast:
50	chr11:62492872..62497117-chr11:62536194..62540986,7	K562	blood:

No data

Variant related genes	Relation type
HNRNPUL2	TF binding region
TTC9C	TF binding region
ENSG00000149016	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000168002	Chromatin interaction
ENSG00000254964	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000168569	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000149489	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000256690	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000162236	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000185475	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11822922	1.00[EUR][1000 genomes]
rs12273912	1.00[EUR][1000 genomes]
rs1787724	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2510538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584915	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584917	0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2730030	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2956139	1.00[EUR][1000 genomes]
rs2958240	1.00[EUR][1000 genomes]
rs4387351	1.00[TSI][hapmap]
rs481272	0.88[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs482331	0.82[ASW][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs489275	1.00[EUR][1000 genomes]
rs4963309	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs506132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs507101	0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs514401	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs518780	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs519473	0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs560618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs561385	0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs56226867	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs564587	0.82[ASW][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs572513	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs573146	0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57338459	1.00[EUR][1000 genomes]
rs575134	0.84[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs577071	1.00[EUR][1000 genomes]
rs57858466	1.00[EUR][1000 genomes]
rs592337	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs595108	1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs646194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs692773	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs694678	1.00[EUR][1000 genomes]
rs73487834	1.00[EUR][1000 genomes]
rs73487878	1.00[EUR][1000 genomes]
rs73487879	1.00[EUR][1000 genomes]
rs73487880	1.00[EUR][1000 genomes]
rs73490026	1.00[EUR][1000 genomes]
rs73502133	1.00[EUR][1000 genomes]

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	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers 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 miRNA target site	489 gene(s)	inside rSNPs	diseases
5	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
6	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
7	nsv348	chr11:62474450-62519712	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs486451	C11orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:144 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62489600-62493800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr11:62491400-62494200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
3	chr11:62491600-62494400	Active TSS	Right Atrium	heart
4	chr11:62491600-62494400	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr11:62491800-62493600	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr11:62491800-62493800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:62491800-62493800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr11:62491800-62493800	Active TSS	Brain Germinal Matrix	brain
9	chr11:62491800-62494000	Transcr. at gene 5' and 3'	A549	lung
10	chr11:62491800-62494200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
11	chr11:62491800-62497200	Active TSS	HSMMtube	muscle
12	chr11:62491800-62497400	Active TSS	Fetal Kidney	kidney
13	chr11:62491800-62497600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:62492000-62493600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr11:62492000-62494000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr11:62492000-62494000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:62492000-62497000	Active TSS	Aorta	Aorta
18	chr11:62492000-62497000	Active TSS	Ovary	ovary
19	chr11:62492000-62497200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:62492000-62497200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr11:62492000-62497200	Active TSS	Fetal Intestine Small	intestine
22	chr11:62492000-62497200	Active TSS	Left Ventricle	heart
23	chr11:62492000-62497400	Active TSS	Psoas Muscle	Psoas
24	chr11:62492000-62497400	Active TSS	Right Ventricle	heart
25	chr11:62492000-62497400	Active TSS	HSMM	muscle
26	chr11:62492000-62497600	Active TSS	Fetal Intestine Large	intestine
27	chr11:62492000-62497800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:62492200-62493600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
29	chr11:62492200-62493600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:62492200-62493600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr11:62492200-62493800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr11:62492200-62493800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr11:62492200-62493800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
34	chr11:62492200-62494000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:62492200-62494000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:62492200-62494200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:62492200-62494200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:62492200-62494200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr11:62492200-62494200	Transcr. at gene 5' and 3'	Fetal Lung	lung
40	chr11:62492200-62494600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:62492200-62497200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:62492200-62497400	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr11:62492200-62497600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:62492200-62497800	Active TSS	NHDF-Ad	bronchial
45	chr11:62492400-62493800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:62492400-62496800	Active TSS	Lung	lung
47	chr11:62492400-62497200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr11:62492400-62497200	Active TSS	Colonic Mucosa	Colon
49	chr11:62492400-62497400	Active TSS	Esophagus	oesophagus
50	chr11:62492600-62493800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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