Variant report

Variant	rs2509962
Chromosome Location	chr11:62309787-62309788
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	chr11:62309566-62314891	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:62309090-62309809	HUVEC	blood vessel:	n/a	n/a
3	RAD21	chr11:62309334-62311061	SK-N-SH	brain:	n/a	chr11:62310404-62310414 chr11:62310784-62310796 chr11:62310626-62310639 chr11:62309670-62309683
4	POLR2A	chr11:62309161-62309819	U87	brain:	n/a	n/a
5	POLR2A	chr11:62308122-62315675	PANC-1	pancreas:	n/a	n/a
6	CTCF	chr11:62309640-62309790	GM12873	blood:	n/a	chr11:62309728-62309736
7	POLR2A	chr11:62309542-62311457	A549	lung:	n/a	n/a
8	WRNIP1	chr11:62309596-62309796	GM12878	blood:	n/a	n/a
9	TCF12	chr11:62309654-62309820	H1-hESC	embryonic stem cell:	n/a	chr11:62309683-62309693
10	FOXA1	chr11:62309603-62309859	T-47D	breast:	n/a	n/a
11	ZEB1	chr11:62309472-62309930	GM12878	blood:	n/a	n/a
12	CHD2	chr11:62309760-62310683	GM12878	blood:	n/a	n/a
13	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
14	POLR2A	chr11:62305310-62315726	PANC-1	pancreas:	n/a	n/a
15	MYC	chr11:62309688-62309799	MCF-7	breast:	n/a	n/a
16	POLR2A	chr11:62309193-62309819	U87	brain:	n/a	n/a
17	CTCF	chr11:62309680-62309830	HEK293	kidney:	n/a	chr11:62309728-62309736
18	FOXA1	chr11:62309553-62309860	T-47D	breast:	n/a	n/a
19	POLR2A	chr11:62309562-62309843	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62307099..62310232-chr11:62431521..62435102,3	MCF-7	breast:
2	chr11:62308096..62310247-chr11:62607085..62609349,3	MCF-7	breast:
3	chr11:62280741..62283276-chr11:62309446..62312033,2	MCF-7	breast:
4	chr11:62274579..62277992-chr11:62305357..62311305,7	MCF-7	breast:
5	chr11:62309531..62310169-chr17:16342004..16342679,2	Hela-S3	cervix:
6	chr11:62162599..62165168-chr11:62309068..62312004,2	K562	blood:
7	chr11:62186203..62188452-chr11:62307785..62309927,2	MCF-7	breast:
8	chr11:62190811..62192819-chr11:62308539..62310844,3	MCF-7	breast:
9	chr11:62302214..62306267-chr11:62306898..62310214,3	K562	blood:
10	chr11:62196161..62199633-chr11:62307876..62311334,4	MCF-7	breast:
11	chr11:62271795..62272366-chr11:62309145..62309964,2	MCF-7	breast:
12	chr11:62307451..62310157-chr11:62311156..62312735,2	K562	blood:
13	chr11:62162016..62162977-chr11:62309722..62310803,6	MCF-7	breast:
14	chr11:62263893..62266128-chr11:62309249..62311326,26	MCF-7	breast:
15	chr11:62193890..62196076-chr11:62309053..62312016,2	MCF-7	breast:
16	chr11:62263870..62269326-chr11:62305524..62310974,8	MCF-7	breast:
17	chr11:62161985..62164172-chr11:62309731..62311839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257058	TF binding region
ENSG00000255432	Chromatin interaction
ENSG00000149021	Chromatin interaction
ENSG00000250659	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000175061	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000255446	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2428548	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2428549	0.89[ASN][1000 genomes]
rs2509961	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2509967	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2509982	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2512562	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2512563	0.85[AFR][1000 genomes];0.89[ASN][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
rs2509962	MTA2	cis	Esophagus Mucosa	GTEx
rs2509962	EML3	cis	Esophagus Mucosa	GTEx
rs2509962	EEF1G	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 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	chr11:62303200-62310000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr11:62303400-62310000	Genic enhancers	Fetal Intestine Small	intestine
5	chr11:62303600-62310000	Genic enhancers	Fetal Stomach	stomach
6	chr11:62303800-62310000	Weak transcription	Primary T cells from cord blood	blood
7	chr11:62304000-62310000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr11:62304400-62310000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:62305000-62310000	Enhancers	Placenta	Placenta
10	chr11:62305600-62310000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:62305600-62310000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr11:62305600-62310000	Enhancers	Brain Cingulate Gyrus	brain
13	chr11:62305600-62310400	Enhancers	Small Intestine	intestine
14	chr11:62305600-62311200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:62305800-62310000	Genic enhancers	HepG2	liver
16	chr11:62305800-62311200	Transcr. at gene 5' and 3'	NHEK	skin
17	chr11:62305800-62311600	Enhancers	Pancreas	Pancrea
18	chr11:62305800-62312600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:62306000-62310000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:62306000-62310000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr11:62306000-62310000	Enhancers	K562	blood
22	chr11:62306000-62310200	Enhancers	Brain Substantia Nigra	brain
23	chr11:62306000-62310600	Weak transcription	Thymus	Thymus
24	chr11:62306200-62310200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr11:62306400-62309800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr11:62306400-62310000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:62306400-62310000	Enhancers	Brain Anterior Caudate	brain
28	chr11:62306400-62310400	Enhancers	Primary hematopoietic stem cells	blood
29	chr11:62306400-62312200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr11:62306600-62309800	Enhancers	Fetal Heart	heart
31	chr11:62306600-62310000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr11:62306600-62310400	Enhancers	Liver	Liver
33	chr11:62307000-62309800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:62307000-62310400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr11:62307000-62310400	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr11:62307000-62310600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr11:62307000-62311200	Flanking Active TSS	HMEC	breast
38	chr11:62307000-62311400	Flanking Active TSS	Osteobl	bone
39	chr11:62307000-62312200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr11:62307000-62312600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:62307000-62312600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr11:62307000-62313600	Flanking Active TSS	GM12878-XiMat	blood
43	chr11:62307200-62310000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:62307200-62310400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:62307400-62310000	Enhancers	Ovary	ovary
46	chr11:62307600-62310000	Enhancers	Lung	lung
47	chr11:62307600-62310600	Enhancers	Spleen	Spleen
48	chr11:62308000-62310400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:62308000-62311600	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr11:62308000-62313200	Transcr. at gene 5' and 3'	NHLF	lung

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