Variant report

Variant	rs353413
Chromosome Location	chr19:38453353-38453354
allele	C/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	MTA3	chr19:38452846-38453787	GM12878	blood:	n/a	n/a
2	BCLAF1	chr19:38452845-38453419	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:38452622-38453360	GM12878	blood:	n/a	n/a
4	PAX5	chr19:38452766-38453395	GM12878	blood:	n/a	n/a
5	EP300	chr19:38452907-38453470	GM12878	blood:	n/a	n/a
6	SMC3	chr19:38453275-38453362	GM12878	blood:	n/a	n/a
7	PAX5	chr19:38452743-38453482	GM12878	blood:	n/a	n/a
8	NFIC	chr19:38452586-38453740	GM12878	blood:	n/a	n/a
9	ZNF384	chr19:38452753-38454155	GM12878	blood:	n/a	n/a
10	POU2F2	chr19:38452811-38453505	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38395370..38399266-chr19:38452571..38456602,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268051	TF binding region
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10422056	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11083438	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11083439	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11668384	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12462485	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12610891	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1632177	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643464	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643465	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1643470	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643472	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725468	0.85[EUR][1000 genomes]
rs1725486	0.95[ASN][1000 genomes]
rs1725490	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs241937	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs241940	0.84[EUR][1000 genomes]
rs241941	0.84[EUR][1000 genomes]
rs241942	0.84[EUR][1000 genomes]
rs241943	0.84[EUR][1000 genomes]
rs241944	0.84[EUR][1000 genomes]
rs241946	0.84[EUR][1000 genomes]
rs353405	0.96[EUR][1000 genomes]
rs353406	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353409	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353412	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3894129	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4802134	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4803536	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803566	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6508748	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6508752	0.95[EUR][1000 genomes]
rs697433	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7255551	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8102871	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8103882	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8105694	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8110417	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8111400	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs833915	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs833916	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs856309	0.84[EUR][1000 genomes]
rs861308	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
2	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
3	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
4	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:38444200-38453800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:38444600-38453600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:38444600-38456800	Weak transcription	Colonic Mucosa	Colon
8	chr19:38445200-38456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:38445200-38456400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:38445400-38457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:38446400-38456600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:38449800-38456800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr19:38451000-38454000	Weak transcription	Ovary	ovary
14	chr19:38452000-38454800	Enhancers	NHDF-Ad	bronchial
15	chr19:38452200-38453600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:38452200-38453600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr19:38452200-38454000	Enhancers	HUVEC	blood vessel
18	chr19:38452200-38454000	Enhancers	Osteobl	bone
19	chr19:38452400-38453400	Weak transcription	HSMM	muscle
20	chr19:38452400-38456600	Weak transcription	Primary T cells from cord blood	blood
21	chr19:38452600-38455800	Enhancers	Primary B cells from cord blood	blood
22	chr19:38452800-38453800	Weak transcription	Lung	lung
23	chr19:38452800-38455000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:38452800-38456400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:38453000-38454200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:38453000-38454200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:38453000-38454200	Enhancers	Gastric	stomach
28	chr19:38453000-38455000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:38453000-38456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:38453200-38453400	Enhancers	Esophagus	oesophagus
31	chr19:38453200-38453400	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr19:38453200-38453800	Enhancers	NHLF	lung
33	chr19:38453200-38454000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:38453200-38454000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:38453200-38454000	Enhancers	Small Intestine	intestine
36	chr19:38453200-38454000	Flanking Active TSS	GM12878-XiMat	blood
37	chr19:38453200-38454200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr19:38453200-38454200	Enhancers	Duodenum Mucosa	Duodenum
39	chr19:38453200-38454200	Enhancers	Pancreas	Pancrea
40	chr19:38453200-38454200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr19:38453200-38454200	Enhancers	Spleen	Spleen
42	chr19:38453200-38454200	Enhancers	HepG2	liver
43	chr19:38453200-38454400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:38453200-38454400	Enhancers	Stomach Mucosa	stomach
45	chr19:38453200-38454800	Genic enhancers	Fetal Intestine Small	intestine
46	chr19:38453200-38455000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:38453200-38455000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr19:38453200-38455000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:38453200-38455000	Enhancers	Fetal Intestine Large	intestine
50	chr19:38453200-38455000	Enhancers	Sigmoid Colon	Sigmoid Colon

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