Variant report

Variant	rs3745953
Chromosome Location	chr19:38852357-38852358
allele	G/T
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	SIN3AK20	chr19:38851954-38853308	A549	lung:	n/a	n/a
2	CTCF	chr19:38852351-38852417	GM13976	blood:	n/a	n/a
3	TBL1XR1	chr19:38852179-38852512	K562	blood:	n/a	n/a
4	CTCF	chr19:38852340-38852490	HBMEC	blood vessel:	n/a	n/a
5	ZBTB7A	chr19:38852200-38853161	ECC-1	luminal epithelium:	n/a	chr19:38852940-38852947
6	TCF12	chr19:38850909-38853674	A549	lung:	n/a	chr19:38852144-38852154
7	SIN3AK20	chr19:38852256-38853491	PANC-1	pancreas:	n/a	n/a
8	REST	chr19:38851925-38852535	A549	lung:	n/a	n/a
9	CTCF	chr19:38852340-38852490	BJ	skin:	n/a	n/a
10	TBP	chr19:38852266-38853432	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr19:38852300-38852450	A549	lung:	n/a	n/a
12	EGR1	chr19:38852327-38852783	K562	blood:	n/a	chr19:38852637-38852647 chr19:38852617-38852630 chr19:38852617-38852630 chr19:38852616-38852631 chr19:38852621-38852631 chr19:38852515-38852525 chr19:38852743-38852756 chr19:38852617-38852631
13	CTCF	chr19:38852300-38852450	BJ	skin:	n/a	n/a
14	CTCF	chr19:38852353-38852517	GM19238	blood:	n/a	n/a
15	UBTF	chr19:38851861-38852557	K562	blood:	n/a	n/a
16	CTCF	chr19:38852340-38852490	HPAF	blood vessel:	n/a	n/a
17	BACH1	chr19:38852274-38852538	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:38852340-38852490	AG10803	skin:	n/a	n/a
19	CTCF	chr19:38852300-38852450	GM12864	blood:	n/a	n/a
20	BCL3	chr19:38851416-38853478	A549	lung:	n/a	chr19:38852942-38852951
21	CTCF	chr19:38852300-38852450	HUVEC	blood vessel:	n/a	n/a
22	CTCF	chr19:38852320-38852470	HPAF	blood vessel:	n/a	n/a
23	MAX	chr19:38852205-38853268	H1-hESC	embryonic stem cell:	n/a	chr19:38852622-38852632
24	CTCF	chr19:38852340-38852490	HMF	breast:	n/a	n/a
25	POLR2A	chr19:38852246-38853516	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr19:38852334-38852506	Hela-S3	cervix:	n/a	n/a
27	MAX	chr19:38852263-38853520	K562	blood:	n/a	chr19:38852622-38852632
28	CTCF	chr19:38852320-38852470	HEEpiC	esophagus:	n/a	n/a
29	CTCF	chr19:38852320-38852470	GM12874	blood:	n/a	n/a
30	CTCF	chr19:38852220-38852370	GM12872	blood:	n/a	n/a
31	POLR2A	chr19:38852320-38852594	A549	lung:	n/a	n/a
32	HMGN3	chr19:38852221-38853464	K562	blood:	n/a	n/a
33	MYC	chr19:38852285-38853478	K562	blood:	n/a	chr19:38852622-38852632
34	CTCF	chr19:38852300-38852450	GM12866	blood:	n/a	n/a
35	SP1	chr19:38852053-38853642	A549	lung:	n/a	chr19:38852912-38852923 chr19:38852970-38852980 chr19:38852971-38852980 chr19:38852681-38852691 chr19:38852622-38852632 chr19:38852637-38852647 chr19:38852618-38852632 chr19:38852636-38852648 chr19:38852623-38852632 chr19:38852970-38852979 chr19:38852969-38852981 chr19:38852681-38852691 chr19:38852621-38852633 chr19:38852970-38852980 chr19:38852939-38852946 chr19:38852638-38852647 chr19:38852637-38852647 chr19:38852200-38852210 chr19:38852636-38852648 chr19:38852633-38852647 chr19:38852637-38852646 chr19:38852622-38852631 chr19:38852940-38852952 chr19:38852638-38852647
36	CTCF	chr19:38852340-38852490	HRPEpiC	eye:	n/a	n/a
37	CTCF	chr19:38852255-38852606	K562	blood:	n/a	chr19:38852510-38852523
38	CTCF	chr19:38852340-38852490	GM12866	blood:	n/a	n/a
39	CTCF	chr19:38852240-38852390	GM12871	blood:	n/a	n/a
40	CTCF	chr19:38852173-38852534	K562	blood:	n/a	chr19:38852510-38852523
41	FOXA2	chr19:38852019-38853279	A549	lung:	n/a	n/a
42	CTCF	chr19:38852320-38852470	AG04450	lung:	n/a	n/a
43	CTCF	chr19:38852320-38852470	Caco-2	colon:	n/a	n/a
44	CTCF	chr19:38852320-38852470	HMEC	breast:	n/a	n/a
45	ZNF263	chr19:38851732-38852408	K562	blood:	n/a	n/a
46	POLR2A	chr19:38852255-38852585	ECC-1	luminal epithelium:	n/a	n/a
47	CTCF	chr19:38852320-38852470	HBMEC	blood vessel:	n/a	n/a
48	CTCF	chr19:38852280-38852430	NHDF-neo	bronchial:	n/a	n/a
49	CTCF	chr19:38852240-38852390	Hela-S3	cervix:	n/a	n/a
50	E2F6	chr19:38852242-38852482	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38843850..38848913-chr19:38849820..38852865,6	K562	blood:
2	chr19:38794216..38796351-chr19:38852337..38854290,3	MCF-7	breast:
3	chr19:38851531..38855576-chr19:38863499..38866575,5	MCF-7	breast:
4	chr19:38745341..38747261-chr19:38850863..38853246,2	K562	blood:
5	chr19:38851019..38853857-chr19:38863435..38867110,13	MCF-7	breast:
6	chr19:38851827..38854715-chr19:38877414..38880419,4	K562	blood:
7	chr19:38851103..38853998-chr19:38877778..38880419,3	K562	blood:
8	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
9	chr19:38755112..38757929-chr19:38851639..38853560,2	MCF-7	breast:
10	chr19:38826255..38829380-chr19:38850634..38854376,3	MCF-7	breast:
11	chr19:38851022..38852568-chr5:122434797..122437026,2	MCF-7	breast:
12	chr19:36629391..36631341-chr19:38851035..38853209,2	MCF-7	breast:
13	chr19:38826766..38829028-chr19:38851929..38854753,2	K562	blood:
14	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
15	chr19:38831821..38834669-chr19:38850986..38853085,2	MCF-7	breast:
16	chr19:38851829..38853788-chr19:38876902..38878905,2	MCF-7	breast:
17	chr19:38846299..38848988-chr19:38850348..38854198,4	MCF-7	breast:
18	chr19:38845897..38848818-chr19:38850039..38852720,3	K562	blood:
19	chr19:38718872..38720876-chr19:38850703..38853087,2	MCF-7	breast:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000167641	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000061455	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000011332	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1060454	1.00[ASN][1000 genomes]
rs2270092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2286548	0.92[ASN][1000 genomes]
rs2302185	0.84[ASN][1000 genomes]
rs2302187	0.92[ASN][1000 genomes]
rs3745963	0.82[JPT][hapmap]
rs3760884	0.82[JPT][hapmap]
rs3786880	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3786881	0.85[ASN][1000 genomes]
rs3786882	0.85[ASN][1000 genomes]
rs73043012	0.92[ASN][1000 genomes]
rs73043013	0.92[ASN][1000 genomes]
rs73043014	0.92[ASN][1000 genomes]
rs73043015	0.92[ASN][1000 genomes]
rs73043027	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS 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	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38851000-38852400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:38851400-38853400	Active TSS	Hela-S3	cervix
3	chr19:38851800-38852400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr19:38851800-38852400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:38851800-38852400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr19:38851800-38852400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr19:38851800-38852400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:38851800-38852400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
9	chr19:38851800-38852400	Enhancers	Spleen	Spleen
10	chr19:38851800-38852400	Flanking Active TSS	K562	blood
11	chr19:38851800-38852600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:38851800-38852600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:38851800-38852800	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr19:38851800-38853000	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:38852000-38852400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38852000-38852400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:38852000-38852400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:38852000-38852400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
21	chr19:38852000-38852400	Active TSS	Primary hematopoietic stem cells	blood
22	chr19:38852000-38852400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr19:38852000-38852400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:38852000-38852400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
30	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr19:38852000-38852400	Bivalent Enhancer	Fetal Brain Male	brain
32	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
33	chr19:38852000-38852400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr19:38852000-38852400	Bivalent Enhancer	Stomach Mucosa	stomach
36	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr19:38852000-38852400	Flanking Bivalent TSS/Enh	HepG2	liver
38	chr19:38852000-38852400	Flanking Active TSS	HMEC	breast
39	chr19:38852000-38852600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr19:38852000-38852600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
41	chr19:38852000-38852600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
42	chr19:38852000-38852600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
43	chr19:38852000-38853000	Active TSS	Brain Angular Gyrus	brain
44	chr19:38852000-38853200	Active TSS	Brain Anterior Caudate	brain
45	chr19:38852000-38853400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:38852000-38853400	Active TSS	Right Atrium	heart
47	chr19:38852000-38853600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr19:38852000-38853600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
49	chr19:38852000-38853600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
50	chr19:38852200-38852400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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