Variant report

Variant	rs10408452
Chromosome Location	chr19:41258355-41258356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr19:41258308-41258715	GM12878	blood:	n/a	n/a
2	CBX3	chr19:41258250-41258670	K562	blood:	n/a	n/a
3	POLR2A	chr19:41258252-41258449	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:41258210-41258622	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:41258165-41258770	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:41258253-41258622	GM12878	blood:	n/a	n/a
7	ESRRA	chr19:41255212-41258832	GM12878	blood:	n/a	chr19:41255368-41255382 chr19:41256561-41256571 chr19:41256561-41256571 chr19:41256557-41256573
8	WRNIP1	chr19:41258352-41258643	GM12878	blood:	n/a	n/a
9	SIX5	chr19:41255261-41259082	A549	lung:	n/a	n/a
10	ZNF384	chr19:41258130-41258704	GM12878	blood:	n/a	n/a
11	EGR1	chr19:41258253-41258745	K562	blood:	n/a	chr19:41258513-41258527 chr19:41258557-41258571
12	CEBPB	chr19:41258080-41258717	K562	blood:	n/a	n/a
13	POLR2A	chr19:41258107-41258580	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:41255130-41259372	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:41255201-41258657	SK-N-MC	brain:	n/a	n/a
16	RUNX3	chr19:41258231-41258746	GM12878	blood:	n/a	n/a
17	YY1	chr19:41258233-41258499	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:41258321-41259150	HepG2	liver:	n/a	n/a
19	EGR1	chr19:41258311-41258679	K562	blood:	n/a	chr19:41258513-41258527 chr19:41258557-41258571
20	ZNF384	chr19:41258263-41258706	K562	blood:	n/a	n/a
21	POLR2A	chr19:41258092-41258630	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:41258163-41258911	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:41258153-41258671	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr19:41258172-41258706	K562	blood:	n/a	n/a
25	POLR2A	chr19:41258214-41258679	H1-hESC	embryonic stem cell:	n/a	n/a
26	MTA3	chr19:41258145-41258751	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
2	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
3	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
4	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
5	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
6	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
7	chr19:41253829..41256175-chr19:41256460..41259109,2	K562	blood:
8	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
9	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
10	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
11	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
12	chr19:41194241..41198233-chr19:41254859..41260401,9	K562	blood:
13	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
14	chr19:41253320..41258890-chr19:41311950..41315573,6	MCF-7	breast:

No data

Variant related genes	Relation type
C19orf54	TF binding region
SNRPA	TF binding region
ENSG00000269858	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10402565	1.00[AMR][1000 genomes]
rs10408716	1.00[AMR][1000 genomes]
rs10415973	1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10417139	1.00[AMR][1000 genomes]
rs10422737	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12104289	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13347002	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28368968	1.00[AMR][1000 genomes]
rs28609092	1.00[AMR][1000 genomes]
rs28636772	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv1793665	chr19:41249508-41258355	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
4	esv1803061	chr19:41249508-41258355	Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
5	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
6	esv1798663	chr19:41256519-41258355	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
7	esv1799699	chr19:41256519-41258355	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
8	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 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	chr19:41254600-41259200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:41255400-41258600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:41255400-41258600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:41255600-41258600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:41255600-41258800	Active TSS	Gastric	stomach
6	chr19:41255600-41259000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:41255800-41258400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:41255800-41258400	Active TSS	Fetal Kidney	kidney
9	chr19:41255800-41258600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:41255800-41258600	Active TSS	Esophagus	oesophagus
11	chr19:41255800-41258600	Active TSS	GM12878-XiMat	blood
12	chr19:41255800-41258800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:41255800-41258800	Active TSS	Right Ventricle	heart
14	chr19:41255800-41259000	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr19:41256000-41258400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:41256000-41258400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:41256000-41258400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr19:41256000-41258600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:41256000-41258600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:41256000-41258600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr19:41256000-41258600	Active TSS	Ovary	ovary
22	chr19:41256000-41258600	Active TSS	Pancreas	Pancrea
23	chr19:41256000-41258600	Active TSS	HSMM	muscle
24	chr19:41256000-41258800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:41256000-41258800	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr19:41256200-41258400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr19:41256200-41258400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:41256200-41258400	Active TSS	Placenta	Placenta
29	chr19:41256200-41258400	Active TSS	HSMMtube	muscle
30	chr19:41256200-41258600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr19:41256200-41258600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr19:41256200-41258600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:41256200-41258600	Active TSS	Brain Germinal Matrix	brain
34	chr19:41256200-41258600	Active TSS	Fetal Brain Female	brain
35	chr19:41256200-41258800	Active TSS	NHDF-Ad	bronchial
36	chr19:41256200-41259000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr19:41256200-41259000	Active TSS	Fetal Intestine Large	intestine
38	chr19:41256200-41259200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:41256400-41258400	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:41256400-41258400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:41256400-41258600	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr19:41256400-41258600	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:41256400-41258600	Active TSS	HMEC	breast
44	chr19:41256800-41258400	Active TSS	Small Intestine	intestine
45	chr19:41257000-41258800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr19:41257000-41259400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:41257200-41258600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr19:41257200-41258600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr19:41257200-41258600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:41257200-41258600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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