Variant report

Variant	rs2512563
Chromosome Location	chr11:62311249-62311250
allele	C/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	chr11:62310675-62311644	K562	blood:	n/a	n/a
2	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
3	POLR2A	chr11:62310128-62311309	U87	brain:	n/a	n/a
4	POLR2A	chr11:62309566-62314891	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr11:62311120-62311270	AG04449	skin:	n/a	n/a
6	POLR2A	chr11:62309984-62315714	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr11:62309985-62314761	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr11:62309853-62314609	U87	brain:	n/a	n/a
9	POLR2A	chr11:62311164-62312081	K562	blood:	n/a	n/a
10	SIN3AK20	chr11:62310077-62311405	PANC-1	pancreas:	n/a	n/a
11	MAX	chr11:62310115-62311690	MCF-7	breast:	n/a	chr11:62311091-62311106 chr11:62311095-62311104 chr11:62311097-62311113 chr11:62311096-62311103 chr11:62311094-62311105 chr11:62310437-62310446 chr11:62311094-62311104
12	POLR2A	chr11:62308122-62315675	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr11:62310085-62311612	HUVEC	blood vessel:	n/a	n/a
14	JUN	chr11:62309914-62311556	K562	blood:	n/a	n/a
15	EBF1	chr11:62310210-62311296	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:62309542-62311457	A549	lung:	n/a	n/a
17	MXI1	chr11:62309801-62316378	IMR90	lung:	n/a	chr11:62311094-62311103 chr11:62311096-62311105
18	CTCF	chr11:62311180-62311330	HBMEC	blood vessel:	n/a	n/a
19	MAX	chr11:62310132-62311411	A549	lung:	n/a	chr11:62311091-62311106 chr11:62311095-62311104 chr11:62311097-62311113 chr11:62311096-62311103 chr11:62311094-62311105 chr11:62310437-62310446 chr11:62311094-62311104
20	TCF12	chr11:62309836-62311580	A549	lung:	n/a	chr11:62311041-62311051 chr11:62309981-62309988 chr11:62310207-62310214
21	POLR2A	chr11:62310826-62311742	MCF-7	breast:	n/a	n/a
22	POLR2A	chr11:62310730-62311319	A549	lung:	n/a	n/a
23	MAZ	chr11:62309657-62311635	IMR90	lung:	n/a	chr11:62311091-62311106 chr11:62311095-62311104 chr11:62311097-62311113 chr11:62311096-62311103 chr11:62311094-62311105 chr11:62310437-62310446 chr11:62311094-62311104
24	POLR2A	chr11:62305310-62315726	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr11:62310128-62314443	U87	brain:	n/a	n/a
26	BCL3	chr11:62309863-62311277	A549	lung:	n/a	chr11:62310548-62310557 chr11:62310096-62310105
27	POLR2A	chr11:62309899-62314587	U87	brain:	n/a	n/a
28	POLR2A	chr11:62310847-62311478	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr11:62309950-62315228	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr11:62310440-62311371	HL-60	blood:	n/a	n/a
31	CHD1	chr11:62310053-62311668	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62280741..62283276-chr11:62309446..62312033,2	MCF-7	breast:
2	chr11:62310191..62312888-chr11:62358804..62361545,2	MCF-7	breast:
3	chr11:62274579..62277992-chr11:62305357..62311305,7	MCF-7	breast:
4	chr11:62162599..62164110-chr11:62310391..62312004,2	K562	blood:
5	chr11:62191932..62192983-chr11:62310101..62311482,6	MCF-7	breast:
6	chr11:62310407..62313306-chr11:62606623..62609508,2	MCF-7	breast:
7	chr11:62310047..62312919-chr11:62648924..62650473,2	K562	blood:
8	chr11:62310730..62313122-chr11:62436444..62438934,2	MCF-7	breast:
9	chr11:62162599..62165168-chr11:62309068..62312004,2	K562	blood:
10	chr11:62310601..62311437-chr11:62461858..62462386,2	K562	blood:
11	chr11:62196161..62199633-chr11:62307876..62311334,4	MCF-7	breast:
12	chr11:62309955..62311757-chr11:62327769..62328678,8	MCF-7	breast:
13	chr11:62263893..62266128-chr11:62309249..62311326,26	MCF-7	breast:
14	chr11:62189906..62192310-chr11:62310087..62312285,3	K562	blood:
15	chr11:62272391..62274377-chr11:62310109..62312238,2	MCF-7	breast:
16	chr11:62165780..62167539-chr11:62310095..62312002,2	K562	blood:
17	chr11:62193890..62196076-chr11:62309053..62312016,2	MCF-7	breast:
18	chr11:62307451..62310157-chr11:62311156..62312735,2	K562	blood:
19	chr11:62310701..62316525-chr11:62336307..62345701,21	MCF-7	breast:
20	chr11:62201060..62204004-chr11:62310651..62312610,2	MCF-7	breast:
21	chr11:62161985..62164172-chr11:62309731..62311839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257058	TF binding region
ENSG00000255508	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000255446	Chromatin interaction
ENSG00000204922	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1061093	0.84[EUR][1000 genomes]
rs11231138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11231141	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231144	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231145	0.87[EUR][1000 genomes]
rs11231150	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11231151	0.83[EUR][1000 genomes]
rs11231152	0.83[EUR][1000 genomes]
rs11231154	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11231155	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11231156	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11231161	0.96[CEU][hapmap]
rs11553576	0.96[CEU][hapmap]
rs12225213	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs17773169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1801144	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs2428548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428549	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]
rs2428551	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2509961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2509962	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2509967	0.99[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];0.91[YRI][hapmap];0.97[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];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516633	0.88[CHB][hapmap];0.90[YRI][hapmap]
rs2516634	0.81[EUR][1000 genomes]
rs2849030	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs2849031	0.95[CEU][hapmap];0.88[CHB][hapmap];0.80[EUR][1000 genomes]
rs35156678	0.91[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	0.91[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	0.91[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	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	esv3430132	chr11:62310961-62311401	Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2512563	MTA2	cis	Esophagus Mucosa	GTEx
rs2512563	EEF1G	cis	multi-tissue	Pritchard
rs2512563	EML3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:111 , 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	chr11:62305800-62311600	Enhancers	Pancreas	Pancrea
4	chr11:62305800-62312600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:62306400-62312200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr11:62307000-62311400	Flanking Active TSS	Osteobl	bone
7	chr11:62307000-62312200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr11:62307000-62312600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:62307000-62312600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr11:62307000-62313600	Flanking Active TSS	GM12878-XiMat	blood
11	chr11:62308000-62311600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr11:62308000-62313200	Transcr. at gene 5' and 3'	NHLF	lung
13	chr11:62308200-62312200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr11:62308200-62312800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:62308200-62313000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr11:62308200-62313200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:62308400-62312200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:62308400-62313000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:62308400-62313400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr11:62308600-62313200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr11:62309000-62314000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
22	chr11:62309400-62311400	Transcr. at gene 5' and 3'	Esophagus	oesophagus
23	chr11:62309400-62312200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:62309600-62312200	Flanking Active TSS	Right Ventricle	heart
25	chr11:62309600-62312600	Flanking Active TSS	Hela-S3	cervix
26	chr11:62309600-62313200	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr11:62309800-62312000	Active TSS	Psoas Muscle	Psoas
28	chr11:62309800-62312400	Flanking Active TSS	Fetal Heart	heart
29	chr11:62309800-62312400	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr11:62309800-62313200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr11:62309800-62313400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr11:62309800-62315400	Active TSS	Aorta	Aorta
33	chr11:62310000-62311400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr11:62310000-62311400	Flanking Active TSS	Lung	lung
35	chr11:62310000-62311400	Flanking Active TSS	Stomach Mucosa	stomach
36	chr11:62310000-62311400	Flanking Active TSS	NH-A	brain
37	chr11:62310000-62312000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
38	chr11:62310000-62312400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr11:62310000-62312400	Flanking Active TSS	HUVEC	blood vessel
40	chr11:62310000-62312600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:62310000-62312600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr11:62310000-62312600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
43	chr11:62310000-62312600	Flanking Active TSS	HepG2	liver
44	chr11:62310000-62312800	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr11:62310000-62313000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:62310000-62313000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:62310000-62313200	Flanking Active TSS	Placenta	Placenta
48	chr11:62310000-62313400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr11:62310000-62314200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:62310000-62314200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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