Variant report

Variant	rs2053071
Chromosome Location	chr19:39390931-39390932
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	HEY1	chr19:39390488-39391135	HepG2	liver:	n/a	chr19:39390636-39390651
2	RCOR1	chr19:39389872-39391141	GM12878	blood:	n/a	n/a
3	YY1	chr19:39390085-39391001	SK-N-SH_RA	brain:	n/a	chr19:39390434-39390442 chr19:39390660-39390669 chr19:39390431-39390453 chr19:39390102-39390116
4	TCF7L2	chr19:39390259-39390964	Hela-S3	cervix:	n/a	n/a
5	TBP	chr19:39390025-39390987	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:39390541-39391065	GM12892	blood:	n/a	n/a
7	RUNX3	chr19:39389709-39391187	GM12878	blood:	n/a	n/a
8	GABPA	chr19:39389994-39390933	SK-N-SH	brain:	n/a	n/a
9	MAX	chr19:39390003-39391020	K562	blood:	n/a	chr19:39390658-39390668
10	RELA	chr19:39389958-39391134	GM15510	blood:	n/a	chr19:39390581-39390590 chr19:39390581-39390590
11	FOSL2	chr19:39389614-39391535	A549	lung:	n/a	chr19:39390500-39390509 chr19:39391294-39391306
12	SIN3AK20	chr19:39389643-39391273	A549	lung:	n/a	n/a
13	POLR2A	chr19:39390591-39390983	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr19:39390284-39391004	H1-hESC	embryonic stem cell:	n/a	chr19:39390658-39390668
15	E2F6	chr19:39389785-39391002	K562	blood:	n/a	chr19:39390047-39390059 chr19:39390586-39390593 chr19:39390099-39390109 chr19:39390586-39390593 chr19:39390586-39390593 chr19:39390079-39390089 chr19:39390660-39390669
16	CREB1	chr19:39389678-39391128	K562	blood:	n/a	n/a
17	TAF1	chr19:39390026-39391189	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F4	chr19:39390030-39390933	K562	blood:	n/a	chr19:39390047-39390059 chr19:39390586-39390593 chr19:39390099-39390109 chr19:39390586-39390593 chr19:39390586-39390593 chr19:39390079-39390089 chr19:39390660-39390669
19	CREB1	chr19:39389801-39391177	HepG2	liver:	n/a	n/a
20	MXI1	chr19:39390001-39391107	HepG2	liver:	n/a	n/a
21	CBX3	chr19:39389772-39391225	K562	blood:	n/a	n/a
22	JUND	chr19:39390020-39391001	K562	blood:	n/a	chr19:39390500-39390509
23	MAZ	chr19:39390004-39391040	HepG2	liver:	n/a	chr19:39390658-39390668
24	ZBTB7A	chr19:39390409-39391043	ECC-1	luminal epithelium:	n/a	chr19:39390648-39390656
25	MAX	chr19:39389893-39391008	HepG2	liver:	n/a	chr19:39390658-39390668
26	POLR2A	chr19:39390480-39390994	K562	blood:	n/a	n/a
27	POLR2A	chr19:39389896-39391023	U87	brain:	n/a	n/a
28	POLR2A	chr19:39389755-39391240	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:39389945-39391007	PFSK-1	brain:	n/a	n/a
30	MAFK	chr19:39390266-39390998	HepG2	liver:	n/a	chr19:39390537-39390552
31	MXI1	chr19:39389478-39391467	IMR90	lung:	n/a	n/a
32	NFE2	chr19:39390816-39390996	GM12878	blood:	n/a	n/a
33	ELK4	chr19:39390285-39391068	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr19:39390033-39391448	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:39390036-39391069	SK-N-MC	brain:	n/a	n/a
36	YY1	chr19:39390101-39390964	A549	lung:	n/a	chr19:39390434-39390442 chr19:39390660-39390669 chr19:39390431-39390453 chr19:39390102-39390116
37	USF1	chr19:39390081-39391011	SK-N-SH_RA	brain:	n/a	n/a
38	ZNF143	chr19:39390121-39391015	Hela-S3	cervix:	n/a	chr19:39390311-39390320 chr19:39390403-39390421 chr19:39390478-39390487 chr19:39390311-39390329
39	TEAD4	chr19:39390003-39391239	K562	blood:	n/a	chr19:39390897-39390906
40	POLR2A	chr19:39389977-39391065	GM19099	blood:	n/a	n/a
41	POLR2A	chr19:39390070-39391038	MCF10A-Er-Src	breast:	n/a	n/a
42	TBL1XR1	chr19:39390029-39391099	K562	blood:	n/a	n/a
43	POLR2A	chr19:39389795-39391128	H1-neurons	neurons:	n/a	n/a
44	TBP	chr19:39390058-39390965	K562	blood:	n/a	n/a
45	MAX	chr19:39389666-39391080	K562	blood:	n/a	chr19:39390658-39390668
46	NFYA	chr19:39390130-39390944	Hela-S3	cervix:	n/a	chr19:39390494-39390512 chr19:39390499-39390513 chr19:39390498-39390513 chr19:39390501-39390511 chr19:39390500-39390513 chr19:39390498-39390513 chr19:39390502-39390514
47	POLR2A	chr19:39390466-39391039	U87	brain:	n/a	n/a
48	MYC	chr19:39390176-39391358	MCF10A-Er-Src	breast:	n/a	chr19:39390658-39390668
49	MYC	chr19:39390185-39391170	NB4	blood:	n/a	chr19:39390658-39390668
50	FOXA2	chr19:39390002-39390975	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39338733..39343337-chr19:39388774..39392675,12	K562	blood:
2	chr19:39390700..39392797-chr19:39401919..39404314,3	K562	blood:
3	chr19:39320984..39323718-chr19:39390338..39392657,3	K562	blood:
4	chr19:39388836..39392687-chr19:39409083..39412619,5	K562	blood:
5	chr19:39390131..39392480-chr19:39402477..39404053,2	MCF-7	breast:
6	chr19:39388885..39392214-chr19:39419332..39422757,5	MCF-7	breast:
7	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
8	chr19:39218316..39221729-chr19:39388696..39391433,3	K562	blood:
9	chr19:39389410..39392783-chr19:39420988..39423307,4	MCF-7	breast:
10	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
11	chr19:39390485..39392144-chr19:39409724..39411734,2	MCF-7	breast:
12	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:

Variant related genes	Relation type
SIRT2	TF binding region
ENSG00000262484	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11083484	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11879872	0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2241704	1.00[YRI][hapmap]
rs2241705	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs3136641	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs8108039	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 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	chr19:39388800-39391400	Active TSS	HSMM	muscle
2	chr19:39389000-39391200	Active TSS	Small Intestine	intestine
3	chr19:39389200-39391200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr19:39389200-39391400	Active TSS	HSMMtube	muscle
5	chr19:39389200-39391600	Active TSS	NHDF-Ad	bronchial
6	chr19:39389400-39391000	Active TSS	Colon Smooth Muscle	Colon
7	chr19:39389400-39391000	Active TSS	Rectal Smooth Muscle	rectum
8	chr19:39389400-39391200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr19:39389400-39391200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:39389400-39391200	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr19:39389400-39391200	Active TSS	Left Ventricle	heart
12	chr19:39389400-39391200	Active TSS	Lung	lung
13	chr19:39389400-39391400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:39389400-39391400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:39389400-39391400	Active TSS	Psoas Muscle	Psoas
16	chr19:39389400-39391600	Active TSS	Right Atrium	heart
17	chr19:39389400-39391800	Active TSS	NHLF	lung
18	chr19:39389600-39391000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:39389600-39391000	Active TSS	Brain Angular Gyrus	brain
20	chr19:39389600-39391000	Active TSS	Brain Anterior Caudate	brain
21	chr19:39389600-39391000	Active TSS	Brain Hippocampus Middle	brain
22	chr19:39389600-39391000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr19:39389600-39391000	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr19:39389600-39391000	Active TSS	Stomach Mucosa	stomach
25	chr19:39389600-39391200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:39389600-39391200	Active TSS	Muscle Satellite Cultured Cells	--
27	chr19:39389600-39391200	Active TSS	Aorta	Aorta
28	chr19:39389600-39391200	Active TSS	Brain Substantia Nigra	brain
29	chr19:39389600-39391200	Active TSS	Gastric	stomach
30	chr19:39389600-39391400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:39389600-39391400	Active TSS	HMEC	breast
32	chr19:39389600-39391600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr19:39389600-39391600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:39389600-39391600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:39389600-39391600	Active TSS	Ovary	ovary
36	chr19:39389600-39391800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:39389600-39391800	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr19:39389600-39391800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:39389600-39391800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:39389800-39391000	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr19:39389800-39391000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:39389800-39391000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:39389800-39391000	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr19:39389800-39391000	Active TSS	Brain Cingulate Gyrus	brain
45	chr19:39389800-39391000	Active TSS	Brain Germinal Matrix	brain
46	chr19:39389800-39391000	Active TSS	Fetal Heart	heart
47	chr19:39389800-39391000	Active TSS	Fetal Kidney	kidney
48	chr19:39389800-39391000	Active TSS	Fetal Lung	lung
49	chr19:39389800-39391000	Active TSS	Fetal Stomach	stomach
50	chr19:39389800-39391000	Active TSS	Spleen	Spleen

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