Variant report

Variant	rs4753840
Chromosome Location	chr11:108338340-108338341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:404)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:404 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr11:108337951-108338437	MCF-7	breast:	n/a	chr11:108338210-108338222
2	ELK1	chr11:108338031-108338523	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:108337719-108338587	K562	blood:	n/a	n/a
4	EP300	chr11:108338000-108338497	T-47D	breast:	n/a	n/a
5	POLR2A	chr11:108337778-108338477	HUVEC	blood vessel:	n/a	n/a
6	SIN3AK20	chr11:108337835-108338373	H1-hESC	embryonic stem cell:	n/a	n/a
7	GABPA	chr11:108337857-108338472	A549	lung:	n/a	n/a
8	RELA	chr11:108337581-108338821	GM12891	blood:	n/a	n/a
9	FOXM1	chr11:108337622-108338773	GM12878	blood:	n/a	n/a
10	CHD2	chr11:108337931-108338412	HepG2	liver:	n/a	n/a
11	RCOR1	chr11:108337937-108338484	HepG2	liver:	n/a	n/a
12	POLR2A	chr11:108337829-108338526	MCF-7	breast:	n/a	n/a
13	POLR2A	chr11:108337830-108338524	MCF-7	breast:	n/a	n/a
14	TAL1	chr11:108337774-108338473	K562	blood:	n/a	chr11:108338010-108338019
15	POLR2A	chr11:108337719-108338683	GM18505	blood:	n/a	n/a
16	NRF1	chr11:108338276-108338550	GM12878	blood:	n/a	n/a
17	TAF1	chr11:108338074-108338475	PFSK-1	brain:	n/a	n/a
18	ZNF384	chr11:108337647-108338502	K562	blood:	n/a	n/a
19	NFIC	chr11:108337863-108338527	HepG2	liver:	n/a	n/a
20	NFYA	chr11:108337881-108338430	K562	blood:	n/a	n/a
21	POLR2A	chr11:108337432-108338696	HUVEC	blood vessel:	n/a	n/a
22	ATF3	chr11:108337961-108338495	H1-hESC	embryonic stem cell:	n/a	chr11:108338241-108338261 chr11:108338252-108338260 chr11:108338249-108338262
23	NFYB	chr11:108338016-108338486	K562	blood:	n/a	n/a
24	POLR2A	chr11:108337548-108338565	PBDE	blood:	n/a	n/a
25	CTCF	chr11:108338200-108338350	AG04449	skin:	n/a	n/a
26	POLR2A	chr11:108337878-108338505	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:108337828-108338619	Gliobla	brain:	n/a	n/a
28	TAF7	chr11:108337818-108338401	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr11:108337711-108338663	U87	brain:	n/a	n/a
30	TAF1	chr11:108337739-108338481	K562	blood:	n/a	n/a
31	GATA3	chr11:108337873-108338481	T-47D	breast:	n/a	n/a
32	GABPA	chr11:108337712-108338573	A549	lung:	n/a	n/a
33	CEBPB	chr11:108337537-108338446	Hela-S3	cervix:	n/a	n/a
34	SMC3	chr11:108337741-108338497	Hela-S3	cervix:	n/a	n/a
35	MXI1	chr11:108337768-108338447	Hela-S3	cervix:	n/a	n/a
36	HEY1	chr11:108337730-108338560	HepG2	liver:	n/a	chr11:108338207-108338222
37	MAX	chr11:108337965-108338341	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr11:108337716-108338583	NB4	blood:	n/a	n/a
39	RCOR1	chr11:108337921-108338602	GM12878	blood:	n/a	n/a
40	CTCF	chr11:108338185-108338449	Spleen_OC	spleen:	n/a	n/a
41	POLR2A	chr11:108337716-108338631	HL-60	blood:	n/a	n/a
42	RCOR1	chr11:108337869-108338455	K562	blood:	n/a	n/a
43	POLR2A	chr11:108337555-108338584	K562	blood:	n/a	n/a
44	POLR2A	chr11:108337608-108338629	PANC-1	pancreas:	n/a	n/a
45	SIN3AK20	chr11:108337749-108338508	K562	blood:	n/a	n/a
46	REST	chr11:108337339-108338890	H1-neurons	neurons:	n/a	chr11:108338203-108338216 chr11:108338206-108338219
47	MAX	chr11:108337734-108338523	Hela-S3	cervix:	n/a	n/a
48	TAF1	chr11:108337830-108338511	GM12878	blood:	n/a	n/a
49	PML	chr11:108337548-108338742	GM12878	blood:	n/a	n/a
50	CEBPB	chr11:108337505-108338669	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:108338329-108338379	Hela-S3	cervix:	n/a
2	chr11:108338329-108338379	HL-60	blood:	n/a
3	chr11:108338329-108338379	HAEpiC	amniotic membrane:	n/a
4	chr11:108338329-108338379	HRE	kidney:	n/a
5	chr11:108338329-108338379	NT2-D1	testis:	n/a
6	chr11:108338329-108338379	SK-N-SH_RA	brain:	n/a
7	chr11:108338329-108338379	HEEpiC	esophagus:	n/a
8	chr11:108338329-108338379	HRCEpiC	kidney:	n/a
9	chr11:108338329-108338379	H1-hESC	embryonic stem cell:	embryo
10	chr11:108338329-108338379	HCT-116	colon:	n/a
11	chr11:108338329-108338379	PFSK-1	brain:	n/a
12	chr11:108338329-108338379	HRPEpiC	eye:	n/a
13	chr11:108338329-108338379	HCM	heart:	n/a
14	chr11:108338329-108338379	HIPEpiC	eye:	n/a
15	chr11:108338329-108338379	SK-N-MC	brain:	n/a
16	chr11:108338329-108338379	LNCaP	prostate:	n/a
17	chr11:108338329-108338379	HCPEpiC	choroid plexus:	n/a
18	chr11:108338329-108338379	PANC-1	pancreas:	n/a
19	chr11:108338329-108338379	HUVEC	blood vessel:	n/a
20	chr11:108338329-108338379	HPAEpiC	pulmonary alveolar:	n/a
21	chr11:108338329-108338379	MCF10A-Er-Src	breast:	n/a
22	chr11:108338329-108338379	A549	lung:	n/a
23	chr11:108338329-108338379	GM19239	blood:	n/a
24	chr11:108338329-108338379	GM12892	blood:	n/a
25	chr11:108338329-108338379	BJ	skin:	n/a
26	chr11:108338329-108338379	GM12878	blood:	n/a
27	chr11:108338329-108338379	HEK293	kidney:	embryo
28	chr11:108338329-108338379	ovcar-3	ovarian:	n/a
29	chr11:108338329-108338379	PrEC	prostate:	n/a
30	chr11:108338329-108338379	SAEC	small airway:	n/a
31	chr11:108338329-108338379	HCF	heart:	n/a
32	chr11:108338329-108338379	U87	brain:	n/a
33	chr11:108338329-108338379	AoSMC	blood vessel:	n/a
34	chr11:108338329-108338379	NHDF-neo	bronchial:	n/a
35	chr11:108338329-108338379	Jurkat	blood:	n/a
36	chr11:108338329-108338379	AG10803	skin:	n/a
37	chr11:108338329-108338379	IMR90	lung:	fetal
38	chr11:108338329-108338379	Caco-2	colon:	n/a
39	chr11:108338329-108338379	NH-A	brain:	n/a
40	chr11:108338329-108338379	K562	blood:	n/a
41	chr11:108338329-108338379	AG04450	lung:	fetal
42	chr11:108338329-108338379	ProgFib	skin:	n/a
43	chr11:108338329-108338379	HepG2	liver:	n/a
44	chr11:108338329-108338379	Hepatocyte	liver:	n/a
45	chr11:108338329-108338379	AG09309	skin:	n/a
46	chr11:108338329-108338379	RPTEC	kidney:	n/a
47	chr11:108338329-108338379	HNPCEpiC	eye:	n/a
48	chr11:108338329-108338379	GM06990	blood:	n/a
49	chr11:108338329-108338379	GM12891	blood:	n/a
50	chr11:108338329-108338379	T-47D	breast:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:108335947..108339609-chr11:108366598..108369824,4	MCF-7	breast:
2	chr11:108337740..108339717-chr11:108368118..108370036,2	MCF-7	breast:
3	chr11:108336534..108338952-chr17:57918620..57920777,2	MCF-7	breast:
4	chr11:108337791..108338457-chr9:139010698..139011343,2	Hela-S3	cervix:
5	chr11:108092141..108094808-chr11:108335621..108340680,5	K562	blood:
6	chr11:108332946..108340923-chr11:108359972..108371658,26	K562	blood:
7	chr1:62901740..62902708-chr11:108337889..108338532,2	Hela-S3	cervix:
8	chr11:108337767..108338554-chr17:73150319..73150938,2	HCT-116	colon:
9	chr11:108338149..108340861-chr11:108349302..108352849,3	K562	blood:
10	chr11:108337592..108338525-chr17:26971908..26972586,2	NB4	blood:
11	chr11:108337665..108338531-chr14:75593065..75594014,2	Hela-S3	cervix:
12	chr11:108333954..108342521-chr11:108361561..108373383,35	K562	blood:
13	chr11:108337795..108338477-chr19:797197..798066,2	HCT-116	colon:
14	chr11:108337858..108338449-chr15:65588328..65589159,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
C11orf65	TF binding region
C11orf65	CpG island
ENSG00000189159	Chromatin interaction
ENSG00000119638	Chromatin interaction
ENSG00000149311	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000162607	Chromatin interaction
ENSG00000011304	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000238227	Chromatin interaction
ENSG00000149308	Chromatin interaction
ENSG00000259138	Chromatin interaction
ENSG00000178202	Chromatin interaction
ENSG00000007202	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10890837	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890844	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10890845	1.00[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs10890846	0.94[EUR][1000 genomes]
rs11212574	1.00[CHB][hapmap]
rs11212590	1.00[CHB][hapmap]
rs11212595	1.00[CHB][hapmap]
rs11212622	1.00[CHB][hapmap]
rs11212650	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11212653	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11212674	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11828864	0.87[EUR][1000 genomes]
rs12274479	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12278954	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17108024	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1801516	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs3092991	1.00[CEU][hapmap]
rs3092993	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs4753843	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754317	0.94[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4988023	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs4988033	1.00[CHB][hapmap]
rs55930851	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7115351	1.00[CEU][hapmap]
rs7131306	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs72992163	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72992175	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72992191	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72993806	0.87[EUR][1000 genomes]
rs72997833	0.87[EUR][1000 genomes]
rs7396719	0.87[EUR][1000 genomes]
rs7938612	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7947933	0.87[EUR][1000 genomes]

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	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
3	nsv832263	chr11:108183372-108384391	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4753840	CUL5	cis	multi-tissue	Pritchard
rs4753840	NPAT	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108337000-108338600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:108337000-108338600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:108337000-108338600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:108337000-108338600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:108337000-108338600	Active TSS	Duodenum Mucosa	Duodenum
6	chr11:108337000-108338600	Active TSS	Fetal Intestine Large	intestine
7	chr11:108337000-108338800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:108337000-108338800	Active TSS	Colonic Mucosa	Colon
9	chr11:108337000-108338800	Active TSS	Colon Smooth Muscle	Colon
10	chr11:108337000-108338800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr11:108337000-108338800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr11:108337000-108339000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr11:108337000-108339000	Active TSS	Stomach Smooth Muscle	stomach
14	chr11:108337200-108338600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr11:108337200-108338600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr11:108337200-108338600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr11:108337200-108338600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:108337200-108338600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr11:108337200-108338600	Active TSS	Primary hematopoietic stem cells	blood
20	chr11:108337200-108338600	Active TSS	Fetal Intestine Small	intestine
21	chr11:108337200-108338600	Active TSS	Fetal Muscle Trunk	muscle
22	chr11:108337200-108338600	Active TSS	Fetal Stomach	stomach
23	chr11:108337200-108338600	Active TSS	Fetal Thymus	thymus
24	chr11:108337200-108338600	Active TSS	Thymus	Thymus
25	chr11:108337200-108338600	Active TSS	A549	lung
26	chr11:108337200-108338600	Active TSS	HMEC	breast
27	chr11:108337200-108338600	Active TSS	NH-A	brain
28	chr11:108337200-108338800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr11:108337200-108338800	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr11:108337200-108338800	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr11:108337200-108338800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr11:108337200-108338800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:108337200-108338800	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr11:108337200-108338800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:108337200-108338800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:108337200-108338800	Active TSS	Brain Cingulate Gyrus	brain
37	chr11:108337200-108338800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr11:108337200-108338800	Active TSS	Fetal Kidney	kidney
39	chr11:108337200-108338800	Active TSS	Fetal Lung	lung
40	chr11:108337200-108338800	Active TSS	Pancreas	Pancrea
41	chr11:108337200-108338800	Active TSS	Rectal Smooth Muscle	rectum
42	chr11:108337200-108338800	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr11:108337200-108338800	Active TSS	HSMMtube	muscle
44	chr11:108337200-108338800	Active TSS	NHLF	lung
45	chr11:108337200-108339000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:108337200-108339000	Active TSS	Brain Hippocampus Middle	brain
47	chr11:108337200-108339000	Active TSS	Brain Substantia Nigra	brain
48	chr11:108337200-108339000	Active TSS	Fetal Brain Female	brain
49	chr11:108337200-108339000	Active TSS	K562	blood
50	chr11:108337200-108339000	Active TSS	Osteobl	bone

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