Variant report

Variant	rs11538384
Chromosome Location	chr19:41220029-41220030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41219937-41220152	A549	lung:	n/a	n/a
2	ELF1	chr19:41219985-41220569	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:41219866-41220351	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:41220016-41220066	Caco-2	colon:	n/a
2	chr19:41220016-41220066	BE2_C	brain:	n/a
3	chr19:41220016-41220066	Hela-S3	cervix:	n/a
4	chr19:41220016-41220066	RPTEC	kidney:	n/a
5	chr19:41220016-41220066	IMR90	lung:	fetal
6	chr19:41220016-41220066	HCF	heart:	n/a
7	chr19:41220016-41220066	NT2-D1	testis:	n/a
8	chr19:41220016-41220066	U87	brain:	n/a
9	chr19:41220016-41220066	HEK293	kidney:	embryo
10	chr19:41220016-41220066	HL-60	blood:	n/a
11	chr19:41220016-41220066	HPAEpiC	pulmonary alveolar:	n/a
12	chr19:41220016-41220066	HCPEpiC	choroid plexus:	n/a
13	chr19:41220016-41220066	HEEpiC	esophagus:	n/a
14	chr19:41220016-41220066	NHBE	bronchial:	n/a
15	chr19:41220016-41220066	SK-N-SH	brain:	n/a
16	chr19:41220016-41220066	BJ	skin:	n/a
17	chr19:41220016-41220066	AG09319	gingival:	n/a
18	chr19:41220016-41220066	GM12878	blood:	n/a
19	chr19:41220016-41220066	MCF-7	breast:	n/a
20	chr19:41220016-41220066	MCF10A-Er-Src	breast:	n/a
21	chr19:41220016-41220066	GM12892	blood:	n/a
22	chr19:41220016-41220066	NH-A	brain:	n/a
23	chr19:41220016-41220066	HCT-116	colon:	n/a
24	chr19:41220016-41220066	CMK	blood:	n/a
25	chr19:41220016-41220066	HUVEC	blood vessel:	n/a
26	chr19:41220016-41220066	PANC-1	pancreas:	n/a
27	chr19:41220016-41220066	HIPEpiC	eye:	n/a
28	chr19:41220016-41220066	AG10803	skin:	n/a
29	chr19:41220016-41220066	A549	lung:	n/a
30	chr19:41220016-41220066	AG04449	skin:	fetal
31	chr19:41220016-41220066	SK-N-MC	brain:	n/a
32	chr19:41220016-41220066	HMEC	breast:	n/a
33	chr19:41220016-41220066	SK-N-SH_RA	brain:	n/a
34	chr19:41220016-41220066	GM19239	blood:	n/a
35	chr19:41220016-41220066	LNCaP	prostate:	n/a
36	chr19:41220016-41220066	AG04450	lung:	fetal
37	chr19:41220016-41220066	ProgFib	skin:	n/a
38	chr19:41220016-41220066	PrEC	prostate:	n/a
39	chr19:41220016-41220066	SAEC	small airway:	n/a
40	chr19:41220016-41220066	GM12891	blood:	n/a
41	chr19:41220016-41220066	HepG2	liver:	n/a
42	chr19:41220016-41220066	PFSK-1	brain:	n/a
43	chr19:41220016-41220066	Hepatocyte	liver:	n/a
44	chr19:41220016-41220066	HRE	kidney:	n/a
45	chr19:41220016-41220066	NB4	blood:	n/a
46	chr19:41220016-41220066	Jurkat	blood:	n/a
47	chr19:41220016-41220066	HRPEpiC	eye:	n/a
48	chr19:41220016-41220066	ovcar-3	ovarian:	n/a
49	chr19:41220016-41220066	HNPCEpiC	eye:	n/a
50	chr19:41220016-41220066	HRCEpiC	kidney:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41219466..41223288-chr19:41281896..41285456,5	MCF-7	breast:
2	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
3	chr19:41213611..41215968-chr19:41219093..41222083,3	MCF-7	breast:
4	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
5	chr19:41219692..41221966-chr19:41769353..41771568,2	MCF-7	breast:
6	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
7	chr19:40949565..40951989-chr19:41219354..41222014,2	K562	blood:
8	chr19:41195568..41198287-chr19:41219071..41220657,2	K562	blood:
9	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
10	chr19:40948713..40950768-chr19:41219384..41222098,2	K562	blood:
11	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
12	chr19:41193720..41198590-chr19:41218677..41224410,19	MCF-7	breast:
13	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:

No data

Variant related genes	Relation type
ITPKC	TF binding region
ITPKC	CpG island
ENSG00000077312	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000223284	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000167565	Chromatin interaction

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

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

rs_ID	r²[population]
rs4802083	0.89[EUR][1000 genomes]
rs4802084	1.00[EUR][1000 genomes]
rs4803357	0.96[EUR][1000 genomes]
rs4803359	1.00[EUR][1000 genomes]
rs4803362	0.82[EUR][1000 genomes]
rs62621363	0.82[EUR][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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 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	chr19:41197200-41220200	Weak transcription	Fetal Heart	heart
2	chr19:41197200-41220600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:41197400-41220200	Weak transcription	HUVEC	blood vessel
4	chr19:41197600-41220200	Weak transcription	Psoas Muscle	Psoas
5	chr19:41205400-41220200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:41208800-41220200	Weak transcription	Stomach Mucosa	stomach
7	chr19:41208800-41221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:41209200-41220200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:41210800-41220200	Weak transcription	Fetal Brain Male	brain
10	chr19:41210800-41220200	Weak transcription	K562	blood
11	chr19:41211400-41220200	Weak transcription	Hela-S3	cervix
12	chr19:41211400-41220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:41211400-41220400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:41211800-41220200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:41211800-41220200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:41212200-41220400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:41212200-41220600	Weak transcription	Aorta	Aorta
18	chr19:41212400-41220200	Weak transcription	Esophagus	oesophagus
19	chr19:41212600-41220200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:41212600-41220400	Weak transcription	Small Intestine	intestine
21	chr19:41214600-41220200	Weak transcription	HepG2	liver
22	chr19:41215400-41220200	Weak transcription	Fetal Kidney	kidney
23	chr19:41215600-41220200	Weak transcription	HSMM	muscle
24	chr19:41216000-41220200	Weak transcription	Primary T cells from cord blood	blood
25	chr19:41216200-41220200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:41216200-41220200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:41216200-41220200	Weak transcription	Osteobl	bone
28	chr19:41216400-41220200	Weak transcription	Colonic Mucosa	Colon
29	chr19:41216600-41220200	Weak transcription	Brain Substantia Nigra	brain
30	chr19:41216800-41220400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:41217200-41220200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:41217600-41220200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:41217600-41220400	Weak transcription	Fetal Lung	lung
34	chr19:41217800-41220200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr19:41217800-41220200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:41217800-41220200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr19:41217800-41220200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:41217800-41220200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:41218000-41220200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:41218200-41220400	Weak transcription	Ovary	ovary
41	chr19:41218400-41220200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:41218800-41220200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:41218800-41220200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr19:41218800-41220200	Weak transcription	Adipose Nuclei	Adipose
45	chr19:41218800-41220200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:41218800-41220400	Enhancers	Primary T cells fromperipheralblood	blood
47	chr19:41218800-41220400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr19:41219000-41220200	Weak transcription	Liver	Liver
49	chr19:41219000-41220200	Weak transcription	Fetal Brain Female	brain
50	chr19:41219000-41220200	Genic enhancers	Fetal Muscle Trunk	muscle

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