Variant report

Variant	rs3758666
Chromosome Location	chr11:47236294-47236295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47235661-47238386	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:47235849-47237200	GM10847	blood:	n/a	n/a
3	POLR2A	chr11:47235775-47238203	GM18505	blood:	n/a	n/a
4	STAT1	chr11:47235643-47237256	Hela-S3	cervix:	n/a	chr11:47236472-47236483 chr11:47236474-47236483 chr11:47236473-47236482
5	MXI1	chr11:47235899-47237245	GM12878	blood:	n/a	n/a
6	HDAC2	chr11:47235772-47237207	MCF-7	breast:	n/a	n/a
7	REST	chr11:47235786-47237254	HL-60	blood:	n/a	chr11:47236447-47236460 chr11:47236821-47236834
8	RFX5	chr11:47235752-47236714	GM12878	blood:	n/a	n/a
9	E2F4	chr11:47235873-47236863	GM12878	blood:	n/a	chr11:47236461-47236470 chr11:47236547-47236558 chr11:47236548-47236555 chr11:47236549-47236560 chr11:47236408-47236420 chr11:47236548-47236556 chr11:47236548-47236559 chr11:47236547-47236557 chr11:47236548-47236556
10	POLR2A	chr11:47235785-47237201	GM12878	blood:	n/a	n/a
11	MAX	chr11:47235712-47237123	MCF-7	breast:	n/a	n/a
12	USF1	chr11:47236152-47236494	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:47235758-47238192	GM18951	blood:	n/a	n/a
14	POLR2A	chr11:47235815-47237300	GM19193	blood:	n/a	n/a
15	E2F6	chr11:47235674-47237166	H1-hESC	embryonic stem cell:	n/a	chr11:47236461-47236470 chr11:47236547-47236558 chr11:47236548-47236555 chr11:47236408-47236420 chr11:47236548-47236556 chr11:47236549-47236560 chr11:47236548-47236559 chr11:47236547-47236557 chr11:47236548-47236556
16	USF1	chr11:47235959-47236675	SK-N-SH	brain:	n/a	n/a
17	SRF	chr11:47235591-47237042	MCF-7	breast:	n/a	n/a
18	USF1	chr11:47236224-47236496	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:47236189-47237772	HepG2	liver:	n/a	n/a
20	ZKSCAN1	chr11:47235833-47236954	Hela-S3	cervix:	n/a	n/a
21	MYC	chr11:47235765-47237005	MCF10A-Er-Src	breast:	n/a	n/a
22	ZNF384	chr11:47235536-47236584	K562	blood:	n/a	n/a
23	CREB1	chr11:47235564-47237283	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:47236247-47237298	K562	blood:	n/a	n/a
25	STAT3	chr11:47235656-47237135	MCF10A-Er-Src	breast:	n/a	chr11:47236474-47236483 chr11:47236473-47236482
26	POLR2A	chr11:47236127-47237144	PFSK-1	brain:	n/a	n/a
27	PAX5	chr11:47236211-47236685	GM12892	blood:	n/a	chr11:47236463-47236472
28	ELF1	chr11:47235823-47237038	GM12878	blood:	n/a	n/a
29	E2F4	chr11:47235744-47237043	MCF10A-Er-Src	breast:	n/a	chr11:47236461-47236470 chr11:47236547-47236558 chr11:47236548-47236555 chr11:47236549-47236560 chr11:47236408-47236420 chr11:47236548-47236556 chr11:47236548-47236559 chr11:47236547-47236557 chr11:47236548-47236556
30	IRF1	chr11:47236269-47236993	K562	blood:	n/a	chr11:47236407-47236421 chr11:47236431-47236445 chr11:47236481-47236495 chr11:47236971-47236984
31	POLR2A	chr11:47235534-47238703	H1-hESC	embryonic stem cell:	n/a	n/a
32	FOSL2	chr11:47235719-47236843	A549	lung:	n/a	n/a
33	ELF1	chr11:47236238-47237172	K562	blood:	n/a	n/a
34	POLR2A	chr11:47235787-47237343	HL-60	blood:	n/a	n/a
35	HA-E2F1	chr11:47235649-47237214	MCF-7	breast:	n/a	chr11:47236461-47236470 chr11:47236547-47236558 chr11:47236548-47236555 chr11:47236408-47236420 chr11:47236548-47236556 chr11:47236548-47236559 chr11:47236547-47236557 chr11:47236548-47236556
36	NR2F2	chr11:47235746-47237255	MCF-7	breast:	n/a	n/a
37	RFX5	chr11:47235668-47236800	H1-hESC	embryonic stem cell:	n/a	n/a
38	MTA3	chr11:47235575-47238559	GM12878	blood:	n/a	n/a
39	EGR1	chr11:47236226-47237023	MCF-7	breast:	n/a	chr11:47236478-47236492 chr11:47236462-47236475 chr11:47236446-47236460
40	SIN3A	chr11:47235924-47237289	GM12878	blood:	n/a	chr11:47237110-47237119
41	STAT3	chr11:47235605-47237166	Hela-S3	cervix:	n/a	chr11:47236474-47236483 chr11:47236473-47236482
42	TAF1	chr11:47235680-47237033	A549	lung:	n/a	n/a
43	POLR2A	chr11:47235639-47238319	PBDE	blood:	n/a	n/a
44	YY1	chr11:47235837-47236631	SK-N-SH_RA	brain:	n/a	chr11:47236349-47236368 chr11:47236351-47236373 chr11:47236464-47236473 chr11:47236421-47236435
45	TBP	chr11:47235702-47237151	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr11:47235760-47237225	HepG2	liver:	n/a	n/a
47	TCF7L2	chr11:47235803-47237042	HCT-116	colon:	n/a	n/a
48	SMC3	chr11:47235596-47237236	Hela-S3	cervix:	n/a	n/a
49	USF1	chr11:47236036-47236608	A549	lung:	n/a	n/a
50	ZNF384	chr11:47235430-47236500	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47223065..47227984-chr11:47233675..47238356,6	MCF-7	breast:
2	chr11:47205689..47216568-chr11:47232414..47239487,27	MCF-7	breast:
3	chr11:47236058..47237053-chr5:43556605..43557161,2	Hela-S3	cervix:
4	chr11:47235457..47236447-chr12:49109932..49110548,2	Hela-S3	cervix:
5	chr11:47235919..47236544-chr16:2204871..2205402,2	Hela-S3	cervix:
6	chr11:47196838..47200214-chr11:47234555..47238435,7	MCF-7	breast:
7	chr11:47235800..47238158-chr11:47268993..47270943,3	MCF-7	breast:
8	chr11:47235321..47238553-chr11:47290387..47292949,4	K562	blood:
9	chr11:47235849..47236350-chr6:37098700..37099200,2	Hela-S3	cervix:
10	chr11:47226100..47227743-chr11:47235838..47237503,2	MCF-7	breast:
11	chr11:47205217..47215436-chr11:47233934..47241095,26	MCF-7	breast:
12	chr11:47234552..47236757-chr11:47290593..47292750,2	MCF-7	breast:
13	chr11:47235961..47236481-chr15:41694254..41694802,2	Hela-S3	cervix:
14	chr11:47234882..47238296-chr11:47268822..47272499,5	MCF-7	breast:
15	chr11:47235151..47238129-chr11:47286989..47291992,5	MCF-7	breast:
16	chr11:47197774..47202059-chr11:47234538..47239113,7	MCF-7	breast:
17	chr11:47235395..47237642-chr11:47289103..47291887,3	K562	blood:
18	chr11:47234491..47236431-chr11:47278921..47281536,2	K562	blood:
19	chr11:47235548..47236492-chr11:62609128..62609703,3	Hela-S3	cervix:

Variant related genes	Relation type
DDB2	TF binding region
ENSG00000260260	Chromatin interaction
ENSG00000243802	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000137806	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000266540	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000149182	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10501319	0.87[ASN][1000 genomes]
rs10742797	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769248	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838652	0.81[ASN][1000 genomes]
rs10838658	0.84[ASN][1000 genomes]
rs10838662	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838663	0.86[ASN][1000 genomes]
rs10838664	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039080	0.81[ASN][1000 genomes]
rs11039081	0.83[ASN][1000 genomes]
rs11601798	0.87[ASN][1000 genomes]
rs11603373	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12417519	0.84[ASN][1000 genomes]
rs12574410	0.86[ASN][1000 genomes]
rs2087215	0.85[ASN][1000 genomes]
rs2279438	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279439	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922684	0.84[ASN][1000 genomes]
rs4269876	0.84[ASN][1000 genomes]
rs4315028	0.83[ASN][1000 genomes]
rs4498951	0.84[ASN][1000 genomes]
rs4576779	0.83[ASN][1000 genomes]
rs4587689	0.84[ASN][1000 genomes]
rs4752965	0.86[ASN][1000 genomes]
rs4752969	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61896133	0.84[ASN][1000 genomes]
rs61896136	0.84[ASN][1000 genomes]
rs61897844	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61897857	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6485726	0.81[ASN][1000 genomes]
rs7112854	0.84[ASN][1000 genomes]
rs7114683	0.81[ASN][1000 genomes]
rs7127741	0.81[ASN][1000 genomes]
rs7130006	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7937410	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7940240	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7950753	0.81[ASN][1000 genomes]
rs7951979	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs901747	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs923324	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47235200-47236600	Active TSS	Fetal Brain Female	brain
2	chr11:47235400-47236400	Flanking Active TSS	Hela-S3	cervix
3	chr11:47235400-47236800	Active TSS	Brain Angular Gyrus	brain
4	chr11:47235400-47236800	Active TSS	Colonic Mucosa	Colon
5	chr11:47235400-47237600	Active TSS	Rectal Smooth Muscle	rectum
6	chr11:47235600-47236400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr11:47235600-47236400	Active TSS	Right Atrium	heart
8	chr11:47235600-47236400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr11:47235600-47236600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:47235600-47236600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:47235600-47236600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr11:47235600-47236600	Active TSS	Primary T cells from cord blood	blood
13	chr11:47235600-47236600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:47235600-47236600	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr11:47235600-47236600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:47235600-47236600	Active TSS	Adipose Nuclei	Adipose
17	chr11:47235600-47236600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:47235600-47236800	Active TSS	Brain Anterior Caudate	brain
19	chr11:47235600-47236800	Active TSS	Brain Cingulate Gyrus	brain
20	chr11:47235600-47236800	Active TSS	Brain Hippocampus Middle	brain
21	chr11:47235600-47236800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr11:47235600-47236800	Active TSS	Brain Substantia Nigra	brain
23	chr11:47235600-47236800	Active TSS	Right Ventricle	heart
24	chr11:47235600-47237000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr11:47235600-47237000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:47235600-47237000	Active TSS	Fetal Kidney	kidney
27	chr11:47235600-47237000	Active TSS	NHEK	skin
28	chr11:47235600-47237400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr11:47235600-47237400	Active TSS	Thymus	Thymus
30	chr11:47235600-47237600	Active TSS	H1 Cell Line	embryonic stem cell
31	chr11:47235600-47237600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:47235600-47237800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:47235600-47238000	Active TSS	Colon Smooth Muscle	Colon
34	chr11:47235600-47238000	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr11:47235600-47238000	Active TSS	A549	lung
36	chr11:47235600-47238200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr11:47235600-47238200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr11:47235600-47238200	Active TSS	GM12878-XiMat	blood
39	chr11:47235600-47238400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr11:47235600-47238400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr11:47235600-47238400	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr11:47235800-47236400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr11:47235800-47236600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:47235800-47236600	Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr11:47235800-47236600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:47235800-47236600	Active TSS	Liver	Liver
47	chr11:47235800-47236600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr11:47235800-47236600	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr11:47235800-47236800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:47235800-47236800	Active TSS	Primary hematopoietic stem cells short term culture	blood

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