Variant report

Variant	rs2428549
Chromosome Location	chr11:62312394-62312395
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	chr11:62312310-62312397	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr11:62312116-62314807	Hela-S3	cervix:	n/a	chr11:62313812-62313819
3	MAX	chr11:62309970-62316873	A549	lung:	n/a	chr11:62312136-62312143 chr11:62313404-62313414 chr11:62311091-62311106 chr11:62311095-62311104 chr11:62311097-62311113 chr11:62311096-62311103 chr11:62311094-62311105 chr11:62310437-62310446 chr11:62315029-62315039 chr11:62311094-62311104 chr11:62316366-62316375
4	RCOR1	chr11:62312189-62312420	K562	blood:	n/a	n/a
5	CHD2	chr11:62312083-62314886	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:62309566-62314891	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:62312235-62313883	HCT-116	colon:	n/a	n/a
8	EP300	chr11:62311960-62314081	A549	lung:	n/a	chr11:62313696-62313712
9	ZKSCAN1	chr11:62312225-62313630	Hela-S3	cervix:	n/a	n/a
10	MYC	chr11:62312021-62314673	NB4	blood:	n/a	chr11:62312136-62312143 chr11:62313404-62313414
11	POLR2A	chr11:62309984-62315714	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr11:62311622-62315026	ProgFib	skin:	n/a	n/a
13	KAP1	chr11:62312330-62313443	U2OS	brain:	n/a	n/a
14	POLR2A	chr11:62309985-62314761	PFSK-1	brain:	n/a	n/a
15	MAZ	chr11:62312120-62314865	Hela-S3	cervix:	n/a	chr11:62312136-62312143 chr11:62313404-62313414
16	POLR2A	chr11:62309853-62314609	U87	brain:	n/a	n/a
17	FOXA2	chr11:62312304-62312758	A549	lung:	n/a	n/a
18	SIN3AK20	chr11:62311496-62315557	PANC-1	pancreas:	n/a	n/a
19	RELA	chr11:62312033-62312743	GM19099	blood:	n/a	chr11:62312237-62312246 chr11:62312237-62312246
20	SMARCC1	chr11:62311698-62314141	Hela-S3	cervix:	n/a	n/a
21	TBP	chr11:62312179-62312645	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr11:62312335-62313687	Hela-S3	cervix:	n/a	n/a
23	TCF7L2	chr11:62312126-62312666	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr11:62311952-62314626	A549	lung:	n/a	chr11:62312209-62312219
25	RELA	chr11:62312124-62313059	GM18951	blood:	n/a	chr11:62312237-62312246 chr11:62312237-62312246
26	SMARCC2	chr11:62312284-62313296	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr11:62311919-62316972	A549	lung:	n/a	chr11:62313556-62313566 chr11:62314439-62314449 chr11:62315752-62315762
28	POLR2A	chr11:62312017-62314779	Hela-S3	cervix:	n/a	n/a
29	ZNF263	chr11:62312030-62314253	HEK293-T-REx	kidney:	n/a	chr11:62313194-62313203 chr11:62313140-62313149 chr11:62313217-62313226 chr11:62313180-62313201
30	FOXA1	chr11:62312329-62312617	T-47D	breast:	n/a	n/a
31	POLR2A	chr11:62308122-62315675	PANC-1	pancreas:	n/a	n/a
32	ZNF263	chr11:62312377-62313407	K562	blood:	n/a	chr11:62313194-62313203 chr11:62313140-62313149 chr11:62313217-62313226 chr11:62313180-62313201
33	POLR2A	chr11:62312146-62314674	K562	blood:	n/a	n/a
34	MAX	chr11:62312052-62314696	K562	blood:	n/a	chr11:62312136-62312143 chr11:62313404-62313414
35	POLR2A	chr11:62311503-62315133	A549	lung:	n/a	n/a
36	MXI1	chr11:62312183-62313293	GM12878	blood:	n/a	n/a
37	MAZ	chr11:62311778-62315881	IMR90	lung:	n/a	chr11:62312136-62312143 chr11:62313404-62313414 chr11:62315029-62315039
38	POLR2A	chr11:62312075-62314696	PFSK-1	brain:	n/a	n/a
39	NR2F2	chr11:62312301-62313524	K562	blood:	n/a	n/a
40	MXI1	chr11:62309801-62316378	IMR90	lung:	n/a	chr11:62311094-62311103 chr11:62311096-62311105
41	REST	chr11:62311980-62312533	A549	lung:	n/a	chr11:62312107-62312125 chr11:62312139-62312152
42	POLR2A	chr11:62311640-62314870	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr11:62311918-62314468	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr11:62312271-62312443	GM12878	blood:	n/a	n/a
45	TCF7L2	chr11:62312174-62313649	HCT-116	colon:	n/a	n/a
46	FOXA2	chr11:62312150-62312869	A549	lung:	n/a	n/a
47	RCOR1	chr11:62312307-62312691	GM12878	blood:	n/a	n/a
48	SIN3AK20	chr11:62312167-62312529	PANC-1	pancreas:	n/a	n/a
49	EBF1	chr11:62311758-62312771	GM12878	blood:	n/a	chr11:62312164-62312174 chr11:62312230-62312241
50	POLR2A	chr11:62312248-62312430	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62311584..62314251-chr11:62412170..62416560,6	MCF-7	breast:
2	chr11:62310191..62312888-chr11:62358804..62361545,2	MCF-7	breast:
3	chr11:62310407..62313306-chr11:62606623..62609508,2	MCF-7	breast:
4	chr11:62310047..62312919-chr11:62648924..62650473,2	K562	blood:
5	chr11:62310730..62313122-chr11:62436444..62438934,2	MCF-7	breast:
6	chr11:62249543..62252001-chr11:62311288..62312995,2	MCF-7	breast:
7	chr11:62159799..62162397-chr11:62312020..62313831,2	MCF-7	breast:
8	chr11:62311884..62313968-chr11:62431155..62433460,2	MCF-7	breast:
9	chr11:62307451..62310157-chr11:62311156..62312735,2	K562	blood:
10	chr11:62310701..62316525-chr11:62336307..62345701,21	MCF-7	breast:
11	chr11:62201060..62204004-chr11:62310651..62312610,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257058	TF binding region
ENSG00000149016	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000255126	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1061093	0.84[EUR][1000 genomes]
rs11231138	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11231141	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231144	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231145	0.87[EUR][1000 genomes]
rs11231150	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11231151	0.83[EUR][1000 genomes]
rs11231152	0.83[EUR][1000 genomes]
rs11231154	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11231155	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11231156	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11231161	0.92[CEU][hapmap]
rs11553576	0.92[CEU][hapmap]
rs12225213	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs17773169	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1801144	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs2428548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428551	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2509961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2509962	0.89[ASN][1000 genomes]
rs2509967	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2509982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516633	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs2516634	0.81[EUR][1000 genomes]
rs2849030	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs2849031	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs35156678	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs35587183	1.00[CHB][hapmap]
rs58720921	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61296092	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7124057	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs71490390	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71490392	0.82[EUR][1000 genomes]
rs72927213	0.83[EUR][1000 genomes]
rs7928833	0.84[EUR][1000 genomes]
rs7930896	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7937146	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7942991	1.00[CHB][hapmap]
rs7943191	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	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
5	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	esv1801128	chr11:62276347-62329897	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers 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	62 gene(s)	inside rSNPs	diseases
7	esv1831183	chr11:62276347-62329897	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic 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	245 gene(s)	inside rSNPs	diseases
9	nsv347	chr11:62297068-62338927	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active 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	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2428549	EEF1G	cis	multi-tissue	Pritchard
rs2428549	MTA2	cis	Esophagus Mucosa	GTEx
rs2428549	EML3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62302400-62312400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:62302400-62315400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:62305800-62312600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:62307000-62312600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:62307000-62312600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr11:62307000-62313600	Flanking Active TSS	GM12878-XiMat	blood
7	chr11:62308000-62313200	Transcr. at gene 5' and 3'	NHLF	lung
8	chr11:62308200-62312800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:62308200-62313000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr11:62308200-62313200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:62308400-62313000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:62308400-62313400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr11:62308600-62313200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
14	chr11:62309000-62314000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
15	chr11:62309600-62312600	Flanking Active TSS	Hela-S3	cervix
16	chr11:62309600-62313200	Flanking Active TSS	Fetal Muscle Trunk	muscle
17	chr11:62309800-62312400	Flanking Active TSS	Fetal Heart	heart
18	chr11:62309800-62312400	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr11:62309800-62313200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr11:62309800-62313400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr11:62309800-62315400	Active TSS	Aorta	Aorta
22	chr11:62310000-62312400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr11:62310000-62312400	Flanking Active TSS	HUVEC	blood vessel
24	chr11:62310000-62312600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:62310000-62312600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr11:62310000-62312600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
27	chr11:62310000-62312600	Flanking Active TSS	HepG2	liver
28	chr11:62310000-62312800	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr11:62310000-62313000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:62310000-62313000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:62310000-62313200	Flanking Active TSS	Placenta	Placenta
32	chr11:62310000-62313400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr11:62310000-62314200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:62310000-62314200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr11:62310200-62315200	Active TSS	Colon Smooth Muscle	Colon
36	chr11:62310400-62315000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:62310400-62315200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:62310400-62315200	Active TSS	Ovary	ovary
39	chr11:62310800-62312400	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
40	chr11:62311000-62312400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:62311000-62312400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
42	chr11:62311000-62312600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:62311000-62312800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr11:62311000-62314800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:62311000-62315200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:62311000-62315200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:62311000-62315200	Active TSS	NHDF-Ad	bronchial
48	chr11:62311200-62312800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:62311200-62313600	Active TSS	Right Atrium	heart
50	chr11:62311200-62314800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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