Variant report

Variant	rs7939766
Chromosome Location	chr11:64881557-64881558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64881288-64881850	H1-hESC	embryonic stem cell:	n/a	n/a
2	EP300	chr11:64880548-64881594	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr11:64879949-64886482	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr11:64881166-64881618	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:64878789-64886874	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:64881093-64881742	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:64878686-64885755	GM12891	blood:	n/a	n/a
8	POLR2A	chr11:64878686-64881679	GM12892	blood:	n/a	n/a
9	POLR2A	chr11:64877568-64887885	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:64881378-64886742	Hela-S3	cervix:	n/a	n/a
11	NFATC1	chr11:64881310-64881673	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:64881239-64886927	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr11:64880680-64881684	ECC-1	luminal epithelium:	n/a	chr11:64881555-64881564 chr11:64881343-64881354
14	POLR2A	chr11:64877637-64885859	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr11:64876227-64885692	HepG2	liver:	n/a	n/a
16	POLR2A	chr11:64881297-64885944	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr11:64881377-64885712	HL-60	blood:	n/a	n/a
18	POLR2A	chr11:64881262-64886939	K562	blood:	n/a	n/a
19	SPI1	chr11:64881511-64881763	HL-60	blood:	n/a	n/a
20	NFIC	chr11:64880617-64881590	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr11:64881331-64883342	HepG2	liver:	n/a	n/a
22	MTA3	chr11:64877414-64881839	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:64876666-64887064	K562	blood:	n/a	n/a
24	POLR2A	chr11:64879095-64885699	A549	lung:	n/a	n/a
25	POLR2A	chr11:64881334-64883170	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr11:64879127-64886880	GM12891	blood:	n/a	n/a
27	POLR2A	chr11:64876945-64886917	PANC-1	pancreas:	n/a	n/a
28	MAX	chr11:64880741-64881667	ECC-1	luminal epithelium:	n/a	chr11:64881555-64881564 chr11:64881343-64881354
29	MAX	chr11:64881003-64881656	K562	blood:	n/a	chr11:64881555-64881564 chr11:64881343-64881354
30	JUN	chr11:64879898-64881698	K562	blood:	n/a	chr11:64881608-64881619
31	NFIC	chr11:64880482-64881647	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr11:64881329-64886973	MCF-7	breast:	n/a	n/a
33	GATA1	chr11:64881207-64881908	PBDE	blood:	n/a	n/a
34	POLR2A	chr11:64881156-64885651	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:64881289-64886927	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr11:64879145-64886802	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64823856..64826495-chr11:64880495..64882277,2	K562	blood:
2	chr11:64880257..64882171-chr11:65269190..65271279,2	MCF-7	breast:
3	chr11:64779861..64784378-chr11:64881512..64885598,8	MCF-7	breast:
4	chr11:64860579..64868255-chr11:64873377..64881831,25	K562	blood:
5	chr11:64881148..64883830-chr11:64986799..64989098,2	MCF-7	breast:
6	chr11:64544538..64546780-chr11:64879402..64882290,2	MCF-7	breast:
7	chr11:64778393..64787449-chr11:64877655..64886980,25	K562	blood:
8	chr11:64552248..64555087-chr11:64879358..64881894,2	MCF-7	breast:
9	chr11:64849359..64854600-chr11:64874292..64883144,16	MCF-7	breast:
10	chr11:64546052..64548172-chr11:64880141..64881711,2	MCF-7	breast:
11	chr11:64880606..64886969-chr11:64935331..64942091,20	K562	blood:
12	chr11:64877702..64891058-chr11:64944203..64957091,32	K562	blood:
13	chr11:64643787..64646984-chr11:64875593..64882466,11	MCF-7	breast:
14	chr11:64875868..64888016-chr11:64945810..64953962,46	MCF-7	breast:
15	chr11:64684925..64687410-chr11:64879641..64882846,3	MCF-7	breast:
16	chr11:64849456..64854518-chr11:64877116..64882654,9	K562	blood:
17	chr11:64778507..64787901-chr11:64877920..64890097,31	K562	blood:
18	chr11:64644806..64648507-chr11:64877927..64882201,4	MCF-7	breast:
19	chr11:64772580..64786543-chr11:64875055..64887722,37	MCF-7	breast:
20	chr11:64878261..64886969-chr11:64935331..64941944,21	K562	blood:
21	chr11:64607104..64613028-chr11:64878466..64882720,9	MCF-7	breast:
22	chr11:64616247..64617841-chr11:64881202..64882719,2	MCF-7	breast:
23	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
24	chr11:64879391..64881748-chr11:64974294..64977624,3	K562	blood:
25	chr11:64644520..64646761-chr11:64879281..64881959,2	K562	blood:
26	chr11:64881095..64883616-chr11:64967076..64970202,3	K562	blood:
27	chr11:64880986..64883460-chr11:65027641..65030397,3	K562	blood:
28	chr11:64606648..64614730-chr11:64876453..64886748,20	MCF-7	breast:
29	chr11:64881531..64883616-chr11:64967521..64970202,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255173	TF binding region
ENSG00000254501	TF binding region
ENSG00000014138	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000249251	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000255200	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000197847	Chromatin interaction
ENSG00000269290	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000254614	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10088	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1149569	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1149570	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1195958	0.82[CEU][hapmap]
rs1195959	0.82[CEU][hapmap]
rs1195975	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1195976	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1195977	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1195978	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196049	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1209621	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1211975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1300836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546532	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17146589	0.82[CEU][hapmap]
rs2370165	0.90[ASN][1000 genomes]
rs2670910	0.82[CEU][hapmap]
rs3819049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850948	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3896078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491465	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930699	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs495820	0.82[CEU][hapmap]
rs495935	0.82[CEU][hapmap]
rs500464	0.82[CEU][hapmap]
rs508375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs531178	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs542175	0.82[CEU][hapmap]
rs550771	0.82[CEU][hapmap]
rs584698	0.82[CEU][hapmap]
rs633671	0.82[CEU][hapmap]
rs664118	0.82[CEU][hapmap]
rs907629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv897712	chr11:64856695-64882789	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	esv3410382	chr11:64878901-64881749	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64879400-64881600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr11:64880600-64881600	Bivalent Enhancer	Fetal Lung	lung
3	chr11:64880800-64881600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:64880800-64881600	Enhancers	Primary hematopoietic stem cells	blood
5	chr11:64880800-64881600	Enhancers	Small Intestine	intestine
6	chr11:64880800-64882000	Enhancers	Spleen	Spleen
7	chr11:64880800-64882200	Enhancers	Pancreas	Pancrea
8	chr11:64880800-64882400	Weak transcription	Lung	lung
9	chr11:64880800-64883400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:64880800-64883600	Weak transcription	A549	lung
11	chr11:64881000-64881600	Enhancers	Primary B cells from peripheral blood	blood
12	chr11:64881000-64881600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr11:64881000-64881600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr11:64881000-64881600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr11:64881000-64881600	Weak transcription	Brain Substantia Nigra	brain
16	chr11:64881000-64881600	Enhancers	Esophagus	oesophagus
17	chr11:64881000-64881600	Enhancers	Fetal Thymus	thymus
18	chr11:64881000-64881600	Flanking Active TSS	HepG2	liver
19	chr11:64881000-64881800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:64881000-64881800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr11:64881000-64882000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:64881000-64882000	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:64881000-64882000	Enhancers	Colonic Mucosa	Colon
24	chr11:64881000-64882000	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr11:64881000-64882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:64881000-64882400	Enhancers	Fetal Heart	heart
27	chr11:64881000-64883000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:64881000-64883000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:64881000-64883000	Weak transcription	Right Ventricle	heart
30	chr11:64881000-64883200	Weak transcription	Gastric	stomach
31	chr11:64881000-64883200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:64881000-64883400	Weak transcription	NHDF-Ad	bronchial
33	chr11:64881000-64883600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:64881000-64883800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:64881000-64884200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:64881000-64884200	Weak transcription	Aorta	Aorta
37	chr11:64881000-64884200	Weak transcription	Right Atrium	heart
38	chr11:64881200-64881600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr11:64881200-64881600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:64881200-64881600	Enhancers	Duodenum Mucosa	Duodenum
41	chr11:64881200-64881600	Enhancers	Fetal Muscle Trunk	muscle
42	chr11:64881200-64881600	Enhancers	Fetal Muscle Leg	muscle
43	chr11:64881200-64881800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:64881200-64881800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr11:64881200-64881800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr11:64881200-64881800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr11:64881200-64882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:64881200-64882000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:64881200-64882000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:64881200-64882000	Enhancers	Brain Germinal Matrix	brain

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