Variant report

Variant	rs2956139
Chromosome Location	chr11:62559301-62559302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:365)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:365 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62556198-62559952	K562	blood:	n/a	n/a
2	GABPA	chr11:62559048-62559632	K562	blood:	n/a	n/a
3	POLR2A	chr11:62558874-62560384	U87	brain:	n/a	n/a
4	TAF1	chr11:62559247-62559640	PFSK-1	brain:	n/a	n/a
5	PML	chr11:62558923-62559646	MCF-7	breast:	n/a	n/a
6	MAX	chr11:62558898-62559655	K562	blood:	n/a	n/a
7	GATA3	chr11:62559179-62559551	T-47D	breast:	n/a	n/a
8	TAF1	chr11:62559038-62559753	A549	lung:	n/a	n/a
9	POLR2A	chr11:62559120-62559629	GM10847	blood:	n/a	n/a
10	SMARCB1	chr11:62558248-62560010	Hela-S3	cervix:	n/a	n/a
11	YY1	chr11:62559074-62559619	GM12891	blood:	n/a	n/a
12	POLR2A	chr11:62558832-62560226	GM12878	blood:	n/a	n/a
13	SP4	chr11:62559143-62559698	H1-hESC	embryonic stem cell:	n/a	chr11:62559540-62559551 chr11:62559540-62559556 chr11:62559509-62559520 chr11:62559480-62559491
14	POLR2A	chr11:62558765-62559965	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:62559281-62559505	IMR90	lung:	n/a	n/a
16	ELF1	chr11:62559076-62559708	A549	lung:	n/a	chr11:62559475-62559486 chr11:62559476-62559485 chr11:62559475-62559486
17	NFATC1	chr11:62558930-62559897	GM12878	blood:	n/a	n/a
18	MXI1	chr11:62559097-62559769	H1-hESC	embryonic stem cell:	n/a	n/a
19	GABPA	chr11:62559131-62559584	Hela-S3	cervix:	n/a	n/a
20	ETS1	chr11:62558954-62559570	K562	blood:	n/a	chr11:62559486-62559499 chr11:62559475-62559484 chr11:62559543-62559554 chr11:62559473-62559483
21	SIN3AK20	chr11:62558928-62559606	PANC-1	pancreas:	n/a	n/a
22	TBP	chr11:62559256-62559602	K562	blood:	n/a	n/a
23	YY1	chr11:62558880-62559832	SK-N-SH	brain:	n/a	n/a
24	TAF1	chr11:62559005-62559575	HepG2	liver:	n/a	n/a
25	POLR2A	chr11:62558820-62559866	ProgFib	skin:	n/a	n/a
26	RUNX3	chr11:62559200-62559703	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:62558516-62559886	HCT-116	colon:	n/a	n/a
28	GABPA	chr11:62558908-62559774	MCF-7	breast:	n/a	n/a
29	ZBTB33	chr11:62559221-62559690	HCT-116	colon:	n/a	n/a
30	POLR2A	chr11:62559148-62559629	K562	blood:	n/a	n/a
31	POLR2A	chr11:62557929-62560314	GM12891	blood:	n/a	n/a
32	REST	chr11:62558976-62559710	HL-60	blood:	n/a	n/a
33	JUND	chr11:62559279-62559479	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAZ	chr11:62559047-62559719	Hela-S3	cervix:	n/a	n/a
35	BCL3	chr11:62558760-62559639	GM12878	blood:	n/a	n/a
36	YY1	chr11:62558988-62559685	GM12878	blood:	n/a	n/a
37	MAX	chr11:62559025-62559918	NB4	blood:	n/a	n/a
38	ELF1	chr11:62559177-62559648	HepG2	liver:	n/a	chr11:62559475-62559486 chr11:62559476-62559485 chr11:62559475-62559486
39	ELK1	chr11:62559205-62559690	GM12878	blood:	n/a	n/a
40	ATF2	chr11:62558996-62559922	GM12878	blood:	n/a	n/a
41	POLR2A	chr11:62556002-62560459	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr11:62555834-62560161	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr11:62558235-62560371	GM12878	blood:	n/a	n/a
44	MAX	chr11:62559054-62559626	K562	blood:	n/a	n/a
45	PAX5	chr11:62558914-62559632	GM12878	blood:	n/a	chr11:62559526-62559535
46	POLR2A	chr11:62559051-62559630	GM12878	blood:	n/a	n/a
47	TAF1	chr11:62559225-62559503	Hela-S3	cervix:	n/a	n/a
48	TAF1	chr11:62559140-62559644	SK-N-SH	brain:	n/a	n/a
49	NFIC	chr11:62559221-62559609	HepG2	liver:	n/a	n/a
50	POLR2A	chr11:62558891-62559653	GM19193	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62557524..62562234-chr11:62648109..62651861,7	MCF-7	breast:
2	chr11:62559078..62559637-chr6:8102019..8102716,2	HCT-116	colon:
3	chr11:62552943..62561747-chr11:62616572..62625876,31	K562	blood:
4	chr1:153940375..153941059-chr11:62558792..62559444,2	HCT-116	colon:
5	chr11:62528206..62530571-chr11:62559091..62560716,2	MCF-7	breast:
6	chr1:149223443..149226268-chr11:62558578..62560961,2	MCF-7	breast:
7	chr11:62445382..62446907-chr11:62557703..62559578,2	MCF-7	breast:
8	chr11:62358650..62362308-chr11:62559226..62561722,3	MCF-7	breast:
9	chr11:62559156..62559891-chr11:62572367..62572916,2	Hela-S3	cervix:
10	chr11:62551512..62560180-chr11:62645894..62651775,24	K562	blood:
11	chr11:62559012..62559818-chr17:1619631..1620393,2	Hela-S3	cervix:
12	chr11:62493399..62495711-chr11:62557116..62560214,4	K562	blood:
13	chr11:62527671..62530483-chr11:62558571..62560981,2	K562	blood:
14	chr11:62431214..62433526-chr11:62556921..62559343,2	MCF-7	breast:
15	chr11:62494172..62498821-chr11:62557548..62561455,7	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM223	TF binding region
ENSG00000168002	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000186594	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000124802	Chromatin interaction
ENSG00000167716	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000255508	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11822922	1.00[EUR][1000 genomes]
rs12273912	1.00[EUR][1000 genomes]
rs1787724	1.00[EUR][1000 genomes]
rs2510538	1.00[EUR][1000 genomes]
rs2584915	1.00[EUR][1000 genomes]
rs2584917	1.00[EUR][1000 genomes]
rs2730030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2730033	1.00[AMR][1000 genomes]
rs2958240	1.00[EUR][1000 genomes]
rs481272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs482331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs486451	1.00[EUR][1000 genomes]
rs489275	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4963309	1.00[EUR][1000 genomes]
rs506132	1.00[EUR][1000 genomes]
rs507101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs514401	1.00[EUR][1000 genomes]
rs518780	1.00[EUR][1000 genomes]
rs519473	1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	1.00[EUR][1000 genomes]
rs560006	1.00[AMR][1000 genomes]
rs560603	1.00[AMR][1000 genomes]
rs560618	1.00[EUR][1000 genomes]
rs561385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs561520	1.00[AMR][1000 genomes]
rs56226867	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs564587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs572513	1.00[EUR][1000 genomes]
rs573146	1.00[EUR][1000 genomes]
rs57338459	1.00[EUR][1000 genomes]
rs575134	1.00[EUR][1000 genomes]
rs577071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57858466	1.00[EUR][1000 genomes]
rs592337	1.00[EUR][1000 genomes]
rs595108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	1.00[EUR][1000 genomes]
rs646194	1.00[EUR][1000 genomes]
rs692773	1.00[EUR][1000 genomes]
rs694678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73487819	1.00[AMR][1000 genomes]
rs73487834	1.00[EUR][1000 genomes]
rs73487878	1.00[EUR][1000 genomes]
rs73487879	1.00[EUR][1000 genomes]
rs73487880	1.00[EUR][1000 genomes]
rs73490026	1.00[EUR][1000 genomes]
rs73502133	1.00[EUR][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	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	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
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	489 gene(s)	inside rSNPs	diseases
5	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
6	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
7	nsv897624	chr11:62549593-62563341	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 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	chr11:62556400-62560200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:62557400-62560000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:62557400-62560400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:62557800-62560200	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr11:62558000-62559600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:62558000-62560200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:62558200-62559400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr11:62558200-62559600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:62558200-62559600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr11:62558200-62559600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:62558200-62559600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr11:62558200-62559600	Transcr. at gene 5' and 3'	Right Atrium	heart
13	chr11:62558200-62560000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:62558200-62560200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
15	chr11:62558200-62560200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
16	chr11:62558400-62559400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:62558400-62559400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr11:62558400-62559600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr11:62558400-62559600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:62558400-62559600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr11:62558400-62559600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:62558400-62559600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:62558400-62559600	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr11:62558400-62559600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr11:62558400-62559600	Active TSS	Fetal Kidney	kidney
26	chr11:62558400-62559600	Active TSS	Left Ventricle	heart
27	chr11:62558400-62559600	Active TSS	Psoas Muscle	Psoas
28	chr11:62558400-62559600	Active TSS	GM12878-XiMat	blood
29	chr11:62558400-62559600	Active TSS	HSMM	muscle
30	chr11:62558400-62559600	Active TSS	HSMMtube	muscle
31	chr11:62558400-62559600	Active TSS	K562	blood
32	chr11:62558400-62559800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr11:62558400-62559800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr11:62558400-62560000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:62558400-62560200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
36	chr11:62558400-62560200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:62558600-62559400	Flanking Active TSS	Fetal Brain Male	brain
38	chr11:62558600-62559400	Transcr. at gene 5' and 3'	Placenta	Placenta
39	chr11:62558600-62559400	Bivalent/Poised TSS	HepG2	liver
40	chr11:62558600-62559600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:62558600-62559600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr11:62558600-62559600	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr11:62558600-62559600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:62558600-62559600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:62558600-62559600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:62558600-62559600	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr11:62558600-62559600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:62558600-62559600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr11:62558600-62559600	Active TSS	Fetal Heart	heart
50	chr11:62558600-62559600	Active TSS	Fetal Intestine Large	intestine

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