Variant report

Variant	rs4420270
Chromosome Location	chr11:9336321-9336322
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	BHLHE40	chr11:9335923-9336667	HepG2	liver:	n/a	chr11:9336300-9336316
2	MYC	chr11:9336002-9336404	MCF-7	breast:	n/a	n/a
3	PBX3	chr11:9335896-9336701	SK-N-SH	brain:	n/a	n/a
4	E2F4	chr11:9336051-9336763	MCF10A-Er-Src	breast:	n/a	chr11:9336286-9336297 chr11:9336470-9336479
5	ELK1	chr11:9335952-9336817	Hela-S3	cervix:	n/a	chr11:9336088-9336097 chr11:9336088-9336097
6	YY1	chr11:9335574-9336753	GM12878	blood:	n/a	n/a
7	RCOR1	chr11:9335955-9336693	HepG2	liver:	n/a	n/a
8	PAX5	chr11:9335572-9336549	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:9335828-9336745	HUVEC	blood vessel:	n/a	n/a
10	REST	chr11:9336269-9336640	SK-N-SH	brain:	n/a	chr11:9336306-9336316 chr11:9336441-9336454
11	SRF	chr11:9336257-9336550	GM12878	blood:	n/a	n/a
12	IRF1	chr11:9335957-9336886	K562	blood:	n/a	n/a
13	POLR2A	chr11:9336276-9336571	A549	lung:	n/a	n/a
14	POLR2A	chr11:9335211-9336857	PBDE	blood:	n/a	n/a
15	POLR2A	chr11:9335784-9337235	PANC-1	pancreas:	n/a	n/a
16	EP300	chr11:9335897-9337123	K562	blood:	n/a	chr11:9336497-9336505 chr11:9336401-9336408 chr11:9336089-9336096
17	CTCF	chr11:9336320-9336610	HFF-Myc	foreskin:	n/a	n/a
18	POLR2A	chr11:9335481-9337154	K562	blood:	n/a	n/a
19	CEBPB	chr11:9335940-9336690	IMR90	lung:	n/a	n/a
20	POLR2A	chr11:9335844-9336857	H1-hESC	embryonic stem cell:	n/a	n/a
21	EP300	chr11:9335977-9336457	HepG2	liver:	n/a	chr11:9336401-9336408 chr11:9336089-9336096
22	TAL1	chr11:9335972-9336664	K562	blood:	n/a	n/a
23	JUN	chr11:9336030-9337512	K562	blood:	n/a	n/a
24	POLR2A	chr11:9335786-9336878	HCT-116	colon:	n/a	n/a
25	ELF1	chr11:9335701-9336738	GM12878	blood:	n/a	chr11:9336398-9336409 chr11:9336399-9336408 chr11:9335740-9335752 chr11:9336398-9336409
26	RXRA	chr11:9335992-9336341	GM12878	blood:	n/a	n/a
27	EGR1	chr11:9335901-9336467	K562	blood:	n/a	chr11:9336323-9336332 chr11:9336400-9336409 chr11:9336088-9336097 chr11:9336192-9336205
28	TAF1	chr11:9335841-9336728	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr11:9335949-9336695	HepG2	liver:	n/a	n/a
30	FOXA1	chr11:9336221-9336488	T-47D	breast:	n/a	n/a
31	MXI1	chr11:9335982-9336548	H1-hESC	embryonic stem cell:	n/a	n/a
32	TBP	chr11:9335946-9336819	GM12878	blood:	n/a	n/a
33	USF2	chr11:9336024-9336834	GM12878	blood:	n/a	chr11:9336300-9336316
34	MXI1	chr11:9335945-9336732	Hela-S3	cervix:	n/a	n/a
35	GABPA	chr11:9336276-9336521	GM12878	blood:	n/a	chr11:9336322-9336333 chr11:9336322-9336336
36	JUND	chr11:9335965-9336655	HepG2	liver:	n/a	n/a
37	MAX	chr11:9335840-9336657	H1-hESC	embryonic stem cell:	n/a	n/a
38	TCF7L2	chr11:9336245-9336830	HEK293	kidney:	n/a	n/a
39	HEY1	chr11:9335783-9337120	K562	blood:	n/a	n/a
40	HNF4A	chr11:9336221-9336616	HepG2	liver:	n/a	n/a
41	POLR2A	chr11:9335896-9337149	GM12891	blood:	n/a	n/a
42	GABPA	chr11:9335916-9336843	SK-N-SH	brain:	n/a	chr11:9336773-9336780 chr11:9336322-9336333 chr11:9336021-9336030 chr11:9336322-9336336 chr11:9336215-9336229
43	SIN3AK20	chr11:9336013-9336666	HepG2	liver:	n/a	n/a
44	RAD21	chr11:9335399-9336743	IMR90	lung:	n/a	n/a
45	YY1	chr11:9336277-9336592	A549	lung:	n/a	n/a
46	EGR1	chr11:9335596-9336789	HCT-116	colon:	n/a	chr11:9336323-9336332 chr11:9336400-9336409 chr11:9336088-9336097 chr11:9336192-9336205
47	MAFK	chr11:9336315-9336692	H1-hESC	embryonic stem cell:	n/a	chr11:9336456-9336472
48	ATF2	chr11:9335892-9336740	GM12878	blood:	n/a	n/a
49	TCF12	chr11:9335351-9337089	A549	lung:	n/a	chr11:9335754-9335764
50	MAX	chr11:9335650-9336867	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9335238..9336588-chr11:9482149..9483111,3	Hela-S3	cervix:
2	chr11:9335962..9338074-chr11:9596330..9598082,2	K562	blood:
3	chr11:9328102..9338305-chr11:9404480..9412498,38	K562	blood:
4	chr11:9335999..9336519-chr7:16685820..16686475,2	Hela-S3	cervix:
5	chr11:9334169..9339249-chr11:9404487..9409469,24	K562	blood:
6	chr1:246670144..246671144-chr11:9335985..9336628,2	HCT-116	colon:
7	chr1:28974718..28975661-chr11:9335971..9336650,2	Hela-S3	cervix:
8	chr11:9335623..9336496-chr11:9405441..9406335,2	NB4	blood:
9	chr11:9283945..9288774-chr11:9332278..9339081,12	K562	blood:
10	chr11:9334187..9337944-chr11:9481178..9484496,6	K562	blood:
11	chr11:9334944..9338278-chr11:9404354..9407861,9	MCF-7	breast:
12	chr11:9334942..9338160-chr11:9405201..9408296,5	MCF-7	breast:
13	chr11:9336246..9336770-chr6:26216163..26217090,2	Hela-S3	cervix:
14	chr11:9333668..9337804-chr11:9478729..9484496,11	K562	blood:

Variant related genes	Relation type
ENSG00000254884	TF binding region
TMEM41B	TF binding region
ENSG00000270103	Chromatin interaction
ENSG00000185420	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000166483	Chromatin interaction
ENSG00000184014	Chromatin interaction
ENSG00000205339	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000136261	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10770012	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10770015	0.89[ASN][1000 genomes]
rs12575328	0.85[ASN][1000 genomes]
rs12793955	0.97[ASN][1000 genomes]
rs12806744	0.89[ASN][1000 genomes]
rs34702749	0.98[ASN][1000 genomes]
rs35378309	0.93[ASN][1000 genomes]
rs4282978	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4300394	0.98[ASN][1000 genomes]
rs4396289	0.86[ASN][1000 genomes]
rs56349194	0.85[ASN][1000 genomes]
rs7114748	0.85[ASN][1000 genomes]
rs72850517	0.86[ASN][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	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
2	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv508617	chr11:9314027-9408562	Flanking Active TSS Weak transcription Enhancers Active TSS Strong 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	27 gene(s)	inside rSNPs	diseases
7	nsv521969	chr11:9334961-9379005	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9332800-9336800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:9333000-9336800	Active TSS	Psoas Muscle	Psoas
3	chr11:9334000-9336400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr11:9334000-9336600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:9334000-9336800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:9334200-9336400	Active TSS	Hela-S3	cervix
7	chr11:9334200-9336400	Active TSS	HSMM	muscle
8	chr11:9334200-9336600	Active TSS	HMEC	breast
9	chr11:9334200-9336600	Active TSS	K562	blood
10	chr11:9334600-9336400	Active TSS	Thymus	Thymus
11	chr11:9334600-9336600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:9334600-9336600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr11:9334600-9336600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr11:9334600-9336600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr11:9334600-9336600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:9334600-9336600	Active TSS	A549	lung
17	chr11:9334600-9336600	Active TSS	HSMMtube	muscle
18	chr11:9334600-9336600	Active TSS	NHDF-Ad	bronchial
19	chr11:9334600-9336600	Active TSS	NHLF	lung
20	chr11:9334600-9337000	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr11:9334600-9337000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr11:9334600-9337000	Active TSS	Right Atrium	heart
23	chr11:9334600-9337400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr11:9334800-9336400	Active TSS	Placenta	Placenta
25	chr11:9334800-9336400	Active TSS	Fetal Thymus	thymus
26	chr11:9334800-9336600	Active TSS	H1 Cell Line	embryonic stem cell
27	chr11:9334800-9336600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:9334800-9336600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr11:9334800-9336600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:9334800-9336600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:9334800-9336600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:9334800-9336600	Active TSS	Fetal Muscle Leg	muscle
33	chr11:9334800-9336600	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr11:9334800-9336600	Active TSS	NHEK	skin
35	chr11:9334800-9336800	Active TSS	Aorta	Aorta
36	chr11:9334800-9336800	Active TSS	Fetal Intestine Large	intestine
37	chr11:9334800-9337200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr11:9334800-9337200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:9335000-9336400	Active TSS	Primary T cells fromperipheralblood	blood
40	chr11:9335000-9336400	Active TSS	Fetal Kidney	kidney
41	chr11:9335000-9336400	Active TSS	Rectal Smooth Muscle	rectum
42	chr11:9335000-9336600	Active TSS	Muscle Satellite Cultured Cells	--
43	chr11:9335000-9336600	Active TSS	Brain Anterior Caudate	brain
44	chr11:9335000-9336600	Active TSS	Brain Cingulate Gyrus	brain
45	chr11:9335000-9336600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr11:9335000-9336600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:9335000-9336600	Active TSS	Colonic Mucosa	Colon
48	chr11:9335000-9336600	Active TSS	Fetal Heart	heart
49	chr11:9335000-9336600	Active TSS	Right Ventricle	heart
50	chr11:9335000-9336600	Active TSS	Stomach Mucosa	stomach

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