Variant report

Variant	rs2428548
Chromosome Location	chr11:62311462-62311463
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	chr11:62310675-62311644	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	chr11:62309566-62314891	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr11:62309984-62315714	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr11:62309985-62314761	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr11:62309853-62314609	U87	brain:	n/a	n/a
7	POLR2A	chr11:62311164-62312081	K562	blood:	n/a	n/a
8	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
9	POLR2A	chr11:62308122-62315675	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr11:62310085-62311612	HUVEC	blood vessel:	n/a	n/a
11	JUN	chr11:62309914-62311556	K562	blood:	n/a	n/a
12	MXI1	chr11:62309801-62316378	IMR90	lung:	n/a	chr11:62311094-62311103 chr11:62311096-62311105
13	TCF12	chr11:62309836-62311580	A549	lung:	n/a	chr11:62311041-62311051 chr11:62309981-62309988 chr11:62310207-62310214
14	POLR2A	chr11:62311277-62311729	MCF-7	breast:	n/a	n/a
15	POLR2A	chr11:62310826-62311742	MCF-7	breast:	n/a	n/a
16	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
17	POLR2A	chr11:62305310-62315726	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr11:62310128-62314443	U87	brain:	n/a	n/a
19	POLR2A	chr11:62309899-62314587	U87	brain:	n/a	n/a
20	POLR2A	chr11:62310847-62311478	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr11:62309950-62315228	SK-N-MC	brain:	n/a	n/a
22	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	chr11:62162599..62164110-chr11:62310391..62312004,2	K562	blood:
4	chr11:62191932..62192983-chr11:62310101..62311482,6	MCF-7	breast:
5	chr11:62310407..62313306-chr11:62606623..62609508,2	MCF-7	breast:
6	chr11:62310047..62312919-chr11:62648924..62650473,2	K562	blood:
7	chr11:62310730..62313122-chr11:62436444..62438934,2	MCF-7	breast:
8	chr11:62162599..62165168-chr11:62309068..62312004,2	K562	blood:
9	chr11:62249543..62252001-chr11:62311288..62312995,2	MCF-7	breast:
10	chr11:62309955..62311757-chr11:62327769..62328678,8	MCF-7	breast:
11	chr11:62189906..62192310-chr11:62310087..62312285,3	K562	blood:
12	chr11:62272391..62274377-chr11:62310109..62312238,2	MCF-7	breast:
13	chr11:62165780..62167539-chr11:62310095..62312002,2	K562	blood:
14	chr11:62193890..62196076-chr11:62309053..62312016,2	MCF-7	breast:
15	chr11:62307451..62310157-chr11:62311156..62312735,2	K562	blood:
16	chr11:62310701..62316525-chr11:62336307..62345701,21	MCF-7	breast:
17	chr11:62201060..62204004-chr11:62310651..62312610,2	MCF-7	breast:
18	chr11:62161985..62164172-chr11:62309731..62311839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257058	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000255446	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000255508	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];0.88[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];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1801144	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs2428549	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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2509962	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2509967	0.98[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];0.96[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];0.96[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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516633	0.88[CHB][hapmap];0.91[YRI][hapmap]
rs2516634	0.81[EUR][1000 genomes]
rs2849030	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs2849031	0.92[CEU][hapmap];0.88[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
rs2428548	EML3	cis	Esophagus Mucosa	GTEx
rs2428548	MTA2	cis	Esophagus Mucosa	GTEx
rs2428548	EEF1G	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 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	chr11:62307000-62312200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr11:62307000-62312600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:62307000-62312600	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr11:62307000-62313600	Flanking Active TSS	GM12878-XiMat	blood
10	chr11:62308000-62311600	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr11:62308000-62313200	Transcr. at gene 5' and 3'	NHLF	lung
12	chr11:62308200-62312200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr11:62308200-62312800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:62308200-62313000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr11:62308200-62313200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:62308400-62312200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:62308400-62313000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:62308400-62313400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr11:62308600-62313200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
20	chr11:62309000-62314000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
21	chr11:62309400-62312200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:62309600-62312200	Flanking Active TSS	Right Ventricle	heart
23	chr11:62309600-62312600	Flanking Active TSS	Hela-S3	cervix
24	chr11:62309600-62313200	Flanking Active TSS	Fetal Muscle Trunk	muscle
25	chr11:62309800-62312000	Active TSS	Psoas Muscle	Psoas
26	chr11:62309800-62312400	Flanking Active TSS	Fetal Heart	heart
27	chr11:62309800-62312400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr11:62309800-62313200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr11:62309800-62313400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr11:62309800-62315400	Active TSS	Aorta	Aorta
31	chr11:62310000-62312000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
32	chr11:62310000-62312400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr11:62310000-62312400	Flanking Active TSS	HUVEC	blood vessel
34	chr11:62310000-62312600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:62310000-62312600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr11:62310000-62312600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
37	chr11:62310000-62312600	Flanking Active TSS	HepG2	liver
38	chr11:62310000-62312800	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr11:62310000-62313000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:62310000-62313000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:62310000-62313200	Flanking Active TSS	Placenta	Placenta
42	chr11:62310000-62313400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr11:62310000-62314200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:62310000-62314200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr11:62310200-62312200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr11:62310200-62315200	Active TSS	Colon Smooth Muscle	Colon
47	chr11:62310400-62311800	Active TSS	Brain Angular Gyrus	brain
48	chr11:62310400-62312000	Weak transcription	Small Intestine	intestine
49	chr11:62310400-62312200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:62310400-62315000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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