Variant report

Variant	rs3745954
Chromosome Location	chr19:38852453-38852454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:145)
CpG islands
(count:61)
Chromatin interactive
region (count:19)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:145 , 50 per page) page: 1 2 3

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	TBL1XR1	chr19:38852179-38852512	K562	blood:	n/a	n/a
3	CTCF	chr19:38852340-38852490	HBMEC	blood vessel:	n/a	n/a
4	CTCF	chr19:38852380-38852530	GM12875	blood:	n/a	chr19:38852510-38852523
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	SMC3	chr19:38852418-38852467	K562	blood:	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	chr19:38852353-38852517	GM19238	blood:	n/a	n/a
14	CTCF	chr19:38852360-38852510	GM12873	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	BCL3	chr19:38851416-38853478	A549	lung:	n/a	chr19:38852942-38852951
20	CTCF	chr19:38852380-38852530	AG04449	skin:	n/a	chr19:38852510-38852523
21	CHD2	chr19:38852389-38852453	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr19:38852358-38852472	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr19:38852320-38852470	HPAF	blood vessel:	n/a	n/a
24	MAX	chr19:38852205-38853268	H1-hESC	embryonic stem cell:	n/a	chr19:38852622-38852632
25	CTCF	chr19:38852340-38852490	HMF	breast:	n/a	n/a
26	POLR2A	chr19:38852246-38853516	H1-neurons	neurons:	n/a	n/a
27	CTCF	chr19:38852380-38852530	AoAF	blood vessel:	n/a	chr19:38852510-38852523
28	POLR2A	chr19:38852334-38852506	Hela-S3	cervix:	n/a	n/a
29	MAX	chr19:38852263-38853520	K562	blood:	n/a	chr19:38852622-38852632
30	CHD2	chr19:38852387-38852743	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr19:38852320-38852470	HEEpiC	esophagus:	n/a	n/a
32	CTCF	chr19:38852320-38852470	GM12874	blood:	n/a	n/a
33	POLR2A	chr19:38852320-38852594	A549	lung:	n/a	n/a
34	HMGN3	chr19:38852221-38853464	K562	blood:	n/a	n/a
35	CTCF	chr19:38852360-38852510	AG09309	skin:	n/a	n/a
36	MYC	chr19:38852285-38853478	K562	blood:	n/a	chr19:38852622-38852632
37	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
38	CTCF	chr19:38852340-38852490	HRPEpiC	eye:	n/a	n/a
39	CTCF	chr19:38852255-38852606	K562	blood:	n/a	chr19:38852510-38852523
40	CTCF	chr19:38852340-38852490	GM12866	blood:	n/a	n/a
41	CTCF	chr19:38852173-38852534	K562	blood:	n/a	chr19:38852510-38852523
42	FOXA2	chr19:38852019-38853279	A549	lung:	n/a	n/a
43	CTCF	chr19:38852320-38852470	AG04450	lung:	n/a	n/a
44	CTCF	chr19:38852320-38852470	Caco-2	colon:	n/a	n/a
45	CTCF	chr19:38852320-38852470	HMEC	breast:	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	chr19:38852382-38852500	GM13977	blood:	n/a	n/a
49	E2F6	chr19:38852242-38852482	K562	blood:	n/a	n/a
50	CTCF	chr19:38852360-38852510	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38852415-38852465	HepG2	liver:	n/a
2	chr19:38852415-38852465	HCT-116	colon:	n/a
3	chr19:38852415-38852465	HRE	kidney:	n/a
4	chr19:38852415-38852465	SAEC	small airway:	n/a
5	chr19:38852415-38852465	SK-N-SH	brain:	n/a
6	chr19:38852415-38852465	AG09309	skin:	n/a
7	chr19:38852415-38852465	HL-60	blood:	n/a
8	chr19:38852415-38852465	CMK	blood:	n/a
9	chr19:38852415-38852465	HNPCEpiC	eye:	n/a
10	chr19:38852415-38852465	Jurkat	blood:	n/a
11	chr19:38852415-38852465	HMEC	breast:	n/a
12	chr19:38852415-38852465	PFSK-1	brain:	n/a
13	chr19:38852415-38852465	HIPEpiC	eye:	n/a
14	chr19:38852415-38852465	Caco-2	colon:	n/a
15	chr19:38852415-38852465	PrEC	prostate:	n/a
16	chr19:38852415-38852465	AG10803	skin:	n/a
17	chr19:38852415-38852465	H1-hESC	embryonic stem cell:	embryo
18	chr19:38852415-38852465	LNCaP	prostate:	n/a
19	chr19:38852415-38852465	U87	brain:	n/a
20	chr19:38852415-38852465	BJ	skin:	n/a
21	chr19:38852415-38852465	ovcar-3	ovarian:	n/a
22	chr19:38852415-38852465	NH-A	brain:	n/a
23	chr19:38852415-38852465	HUVEC	blood vessel:	n/a
24	chr19:38852415-38852465	Hepatocyte	liver:	n/a
25	chr19:38852415-38852465	GM12891	blood:	n/a
26	chr19:38852415-38852465	SKMC	muscle:	n/a
27	chr19:38852415-38852465	ECC-1	luminal epithelium:	n/a
28	chr19:38852415-38852465	MCF10A-Er-Src	breast:	n/a
29	chr19:38852415-38852465	NHDF-neo	bronchial:	n/a
30	chr19:38852415-38852465	AoSMC	blood vessel:	n/a
31	chr19:38852415-38852465	HCPEpiC	choroid plexus:	n/a
32	chr19:38852415-38852465	HCM	heart:	n/a
33	chr19:38852415-38852465	HEEpiC	esophagus:	n/a
34	chr19:38852415-38852465	AG09319	gingival:	n/a
35	chr19:38852415-38852465	MCF-7	breast:	n/a
36	chr19:38852415-38852465	HRCEpiC	kidney:	n/a
37	chr19:38852415-38852465	GM12878	blood:	n/a
38	chr19:38852415-38852465	SK-N-SH_RA	brain:	n/a
39	chr19:38852415-38852465	HPAEpiC	pulmonary alveolar:	n/a
40	chr19:38852415-38852465	SK-N-MC	brain:	n/a
41	chr19:38852415-38852465	AG04449	skin:	fetal
42	chr19:38852415-38852465	GM19239	blood:	n/a
43	chr19:38852415-38852465	HEK293	kidney:	embryo
44	chr19:38852415-38852465	IMR90	lung:	fetal
45	chr19:38852415-38852465	BE2_C	brain:	n/a
46	chr19:38852415-38852465	GM12892	blood:	n/a
47	chr19:38852415-38852465	HAEpiC	amniotic membrane:	n/a
48	chr19:38852415-38852465	NB4	blood:	n/a
49	chr19:38852415-38852465	NHBE	bronchial:	n/a
50	chr19:38852415-38852465	RPTEC	kidney:	n/a

(count:19 , 50 per page) page: 1

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:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGN-2	chr19:38852435-38852575	ENSG00000266963.1

No data

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

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11556992	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12460280	0.80[EUR][1000 genomes]
rs12608599	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12608644	0.87[ASN][1000 genomes]
rs12608722	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12609258	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12610650	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2074982	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302186	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302227	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3745957	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3948666	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4432370	0.95[ASN][1000 genomes]
rs45485196	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55959303	0.86[ASN][1000 genomes]
rs56854837	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58462889	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6508790	0.88[ASN][1000 genomes]
rs72480720	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38851400-38853400	Active TSS	Hela-S3	cervix
2	chr19:38851800-38852600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:38851800-38852600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr19:38851800-38852800	Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr19:38851800-38853000	Bivalent/Poised TSS	Fetal Brain Female	brain
6	chr19:38852000-38852600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr19:38852000-38852600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
8	chr19:38852000-38852600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
9	chr19:38852000-38852600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr19:38852000-38853000	Active TSS	Brain Angular Gyrus	brain
11	chr19:38852000-38853200	Active TSS	Brain Anterior Caudate	brain
12	chr19:38852000-38853400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:38852000-38853400	Active TSS	Right Atrium	heart
14	chr19:38852000-38853600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr19:38852000-38853600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
16	chr19:38852000-38853600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr19:38852200-38852600	Active TSS	Primary monocytes fromperipheralblood	blood
18	chr19:38852200-38852600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:38852200-38852600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:38852200-38852600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:38852200-38852600	Flanking Active TSS	Gastric	stomach
22	chr19:38852200-38852600	Flanking Active TSS	Lung	lung
23	chr19:38852200-38852600	Active TSS	Ovary	ovary
24	chr19:38852200-38852800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:38852200-38852800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr19:38852200-38853000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr19:38852200-38853000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr19:38852200-38853000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
29	chr19:38852200-38853000	Active TSS	Rectal Smooth Muscle	rectum
30	chr19:38852200-38853200	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr19:38852200-38853200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:38852200-38853200	Active TSS	Placenta Amnion	Placenta Amnion
33	chr19:38852200-38853200	Active TSS	GM12878-XiMat	blood
34	chr19:38852200-38853400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr19:38852200-38853400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:38852200-38853400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:38852200-38853400	Active TSS	Aorta	Aorta
38	chr19:38852200-38853400	Active TSS	Esophagus	oesophagus
39	chr19:38852200-38853400	Active TSS	Left Ventricle	heart
40	chr19:38852200-38853400	Flanking Active TSS	Pancreas	Pancrea
41	chr19:38852200-38853400	Active TSS	NH-A	brain
42	chr19:38852200-38853600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:38852200-38853600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:38852200-38853600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:38852200-38853600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:38852200-38853600	Active TSS	Brain Cingulate Gyrus	brain
47	chr19:38852200-38853600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr19:38852200-38853600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr19:38852200-38853600	Flanking Active TSS	Placenta	Placenta
50	chr19:38852200-38853600	Active TSS	Psoas Muscle	Psoas

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