Variant report

Variant	rs353414
Chromosome Location	chr19:38453191-38453192
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

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	BHLHE40	chr19:38452887-38453279	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:38452832-38453318	GM12878	blood:	n/a	n/a
4	PAX5	chr19:38452762-38453257	GM12891	blood:	n/a	n/a
5	BCLAF1	chr19:38452845-38453419	GM12878	blood:	n/a	n/a
6	RUNX3	chr19:38452622-38453360	GM12878	blood:	n/a	n/a
7	PAX5	chr19:38452766-38453395	GM12878	blood:	n/a	n/a
8	FOXM1	chr19:38452758-38453221	GM12878	blood:	n/a	n/a
9	ZEB1	chr19:38452765-38453247	GM12878	blood:	n/a	n/a
10	EP300	chr19:38452907-38453470	GM12878	blood:	n/a	n/a
11	NFIC	chr19:38452832-38453322	GM12878	blood:	n/a	n/a
12	RELA	chr19:38452907-38453332	GM19099	blood:	n/a	n/a
13	BCL11A	chr19:38452825-38453195	GM12878	blood:	n/a	n/a
14	TCF3	chr19:38452768-38453221	GM12878	blood:	n/a	n/a
15	TCF12	chr19:38452898-38453221	GM12878	blood:	n/a	n/a
16	PAX5	chr19:38452838-38453234	GM12892	blood:	n/a	n/a
17	PAX5	chr19:38452990-38453232	GM12891	blood:	n/a	n/a
18	EBF1	chr19:38452845-38453234	GM12878	blood:	n/a	n/a
19	PAX5	chr19:38452743-38453482	GM12878	blood:	n/a	n/a
20	MAX	chr19:38452967-38453289	GM12878	blood:	n/a	n/a
21	NFIC	chr19:38452586-38453740	GM12878	blood:	n/a	n/a
22	PAX5	chr19:38452849-38453278	GM12878	blood:	n/a	n/a
23	EBF1	chr19:38452848-38453264	GM12878	blood:	n/a	n/a
24	FOXM1	chr19:38452697-38453310	GM12878	blood:	n/a	n/a
25	STAT5A	chr19:38452963-38453312	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr19:38452755-38453318	GM12878	blood:	n/a	n/a
27	EP300	chr19:38452893-38453235	GM12878	blood:	n/a	n/a
28	EBF1	chr19:38452915-38453342	GM12878	blood:	n/a	n/a
29	ZNF384	chr19:38452753-38454155	GM12878	blood:	n/a	n/a
30	POU2F2	chr19:38452811-38453505	GM12878	blood:	n/a	n/a
31	PAX5	chr19:38452784-38453340	GM12878	blood:	n/a	n/a
32	RELA	chr19:38452858-38453284	GM12891	blood:	n/a	n/a
33	YY1	chr19:38452992-38453301	GM12878	blood:	n/a	n/a

No data

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

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

No data

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

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10404567	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10415548	0.83[CEU][hapmap]
rs10420746	1.00[CEU][hapmap]
rs1119229	0.87[CEU][hapmap]
rs1643462	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1643463	0.95[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643469	0.98[EUR][1000 genomes]
rs1725469	0.91[ASN][1000 genomes]
rs1725477	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1725478	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725480	0.95[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs1725483	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725485	0.95[EUR][1000 genomes]
rs1725487	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725488	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1725494	0.97[EUR][1000 genomes]
rs1725499	0.83[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs241932	1.00[CEU][hapmap]
rs2544718	0.97[EUR][1000 genomes]
rs35209753	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs353398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353399	1.00[EUR][1000 genomes]
rs353400	1.00[EUR][1000 genomes]
rs353402	1.00[EUR][1000 genomes]
rs353403	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353404	1.00[EUR][1000 genomes]
rs353407	1.00[EUR][1000 genomes]
rs353410	0.83[CEU][hapmap]
rs353411	0.83[CEU][hapmap]
rs353415	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs353416	1.00[EUR][1000 genomes]
rs353417	1.00[EUR][1000 genomes]
rs353419	1.00[EUR][1000 genomes]
rs353420	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353421	1.00[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353424	1.00[EUR][1000 genomes]
rs353425	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353426	0.98[EUR][1000 genomes]
rs353427	1.00[EUR][1000 genomes]
rs353428	0.95[EUR][1000 genomes]
rs353429	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs353430	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3786869	0.82[CEU][hapmap]
rs4239516	0.82[CEU][hapmap]
rs4802135	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4803524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4803551	0.87[CEU][hapmap]
rs4803573	0.87[CEU][hapmap]
rs705491	0.87[CEU][hapmap]
rs705492	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705493	0.87[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs705495	0.87[CEU][hapmap]
rs705500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7258597	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs752878	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs8107341	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8112706	1.00[CEU][hapmap]
rs8113521	0.83[CEU][hapmap]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833896	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs833897	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833898	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833914	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs833926	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs856304	1.00[CEU][hapmap]
rs9304572	0.88[AMR][1000 genomes];0.91[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs353414	ZNF571	cis	multi-tissue	Pritchard
rs353414	WDR87	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

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	chr19:38444000-38453200	Weak transcription	Pancreas	Pancrea
6	chr19:38444200-38453800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:38444600-38453600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:38444600-38456800	Weak transcription	Colonic Mucosa	Colon
9	chr19:38445200-38453200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr19:38445200-38453200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:38445200-38456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:38445200-38456400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:38445400-38457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:38445600-38453200	Weak transcription	Fetal Intestine Large	intestine
15	chr19:38446400-38456600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:38447000-38453200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:38448000-38453200	Weak transcription	Stomach Mucosa	stomach
18	chr19:38449800-38456800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:38450200-38453200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:38450400-38453200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:38450600-38453200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:38451000-38453200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr19:38451000-38453200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:38451000-38453200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:38451000-38454000	Weak transcription	Ovary	ovary
26	chr19:38452000-38454800	Enhancers	NHDF-Ad	bronchial
27	chr19:38452200-38453600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:38452200-38453600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:38452200-38454000	Enhancers	HUVEC	blood vessel
30	chr19:38452200-38454000	Enhancers	Osteobl	bone
31	chr19:38452400-38453200	Weak transcription	A549	lung
32	chr19:38452400-38453200	Enhancers	GM12878-XiMat	blood
33	chr19:38452400-38453200	Weak transcription	NH-A	brain
34	chr19:38452400-38453400	Weak transcription	HSMM	muscle
35	chr19:38452400-38456600	Weak transcription	Primary T cells from cord blood	blood
36	chr19:38452600-38453200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:38452600-38455800	Enhancers	Primary B cells from cord blood	blood
38	chr19:38452800-38453800	Weak transcription	Lung	lung
39	chr19:38452800-38455000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:38452800-38456400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:38453000-38453200	Weak transcription	Fetal Intestine Small	intestine
42	chr19:38453000-38454200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:38453000-38454200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:38453000-38454200	Enhancers	Gastric	stomach
45	chr19:38453000-38455000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:38453000-38456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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