Variant report

Variant	rs353423
Chromosome Location	chr19:38450336-38450337
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	MEF2A	chr19:38450145-38450702	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr19:38450069-38450842	GM12878	blood:	n/a	n/a
3	ZNF384	chr19:38449915-38450825	GM12878	blood:	n/a	n/a
4	NFIC	chr19:38449653-38450785	GM12878	blood:	n/a	n/a
5	EP300	chr19:38450105-38450809	GM12878	blood:	n/a	n/a
6	EBF1	chr19:38449960-38450875	GM12878	blood:	n/a	chr19:38450479-38450490
7	MEF2C	chr19:38450218-38450775	GM12878	blood:	n/a	n/a
8	EBF1	chr19:38450185-38450670	GM12878	blood:	n/a	chr19:38450479-38450490
9	BHLHE40	chr19:38450028-38450743	GM12878	blood:	n/a	n/a
10	NFIC	chr19:38450185-38450676	GM12878	blood:	n/a	n/a
11	EBF1	chr19:38450226-38450614	GM12878	blood:	n/a	chr19:38450479-38450490
12	RUNX3	chr19:38449973-38450576	GM12878	blood:	n/a	n/a
13	MEF2A	chr19:38449853-38450777	GM12878	blood:	n/a	n/a
14	ATF2	chr19:38450269-38450806	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000268051	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10404567	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10415548	0.83[CEU][hapmap]
rs10420746	1.00[CEU][hapmap]
rs1119229	0.87[CEU][hapmap]
rs1643462	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1643463	0.95[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1643467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1643468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1643469	0.98[EUR][1000 genomes]
rs1725469	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1725477	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725478	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725480	0.95[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1725483	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1725485	0.95[EUR][1000 genomes]
rs1725487	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1725488	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725494	0.97[EUR][1000 genomes]
rs1725499	0.83[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs241932	1.00[CEU][hapmap]
rs2544718	0.97[EUR][1000 genomes]
rs35209753	0.87[EUR][1000 genomes]
rs353398	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353399	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353400	1.00[EUR][1000 genomes]
rs353402	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353403	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353404	1.00[EUR][1000 genomes]
rs353407	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353410	0.83[CEU][hapmap]
rs353411	0.83[CEU][hapmap]
rs353414	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]
rs353415	1.00[CEU][hapmap];0.87[YRI][hapmap];0.96[EUR][1000 genomes]
rs353416	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353417	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353419	1.00[EUR][1000 genomes]
rs353420	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353421	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353424	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353425	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353426	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs353427	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs353428	0.95[EUR][1000 genomes]
rs353429	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353430	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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];0.90[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];0.95[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs705493	0.87[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs705495	0.87[CEU][hapmap]
rs705500	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7258597	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs752878	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs8107341	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[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];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833896	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs833897	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833898	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs833914	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs833926	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs856300	0.93[CEU][hapmap]
rs856304	1.00[CEU][hapmap]
rs9304572	0.86[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
rs353423	WDR87	cis	Thyroid	GTEx
rs353423	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
2	chr19:38426600-38450800	Weak transcription	Ovary	ovary
3	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
4	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
5	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
6	chr19:38439600-38453000	Weak transcription	Gastric	stomach
7	chr19:38441400-38456800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38444000-38453200	Weak transcription	Pancreas	Pancrea
9	chr19:38444200-38453800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:38444600-38453600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:38444600-38456800	Weak transcription	Colonic Mucosa	Colon
12	chr19:38445200-38450600	Weak transcription	HSMM	muscle
13	chr19:38445200-38452000	Weak transcription	NH-A	brain
14	chr19:38445200-38453200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:38445200-38453200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:38445200-38456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:38445200-38456400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:38445400-38457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38445600-38451800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:38445600-38453200	Weak transcription	Fetal Intestine Large	intestine
21	chr19:38446400-38456600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:38447000-38452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:38447000-38453200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:38448000-38453200	Weak transcription	Stomach Mucosa	stomach
25	chr19:38448600-38451000	ZNF genes & repeats	A549	lung
26	chr19:38449000-38451400	Weak transcription	Fetal Intestine Small	intestine
27	chr19:38449000-38451600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:38449600-38451000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr19:38449600-38451000	Flanking Active TSS	GM12878-XiMat	blood
30	chr19:38449800-38450400	Enhancers	Duodenum Mucosa	Duodenum
31	chr19:38449800-38451000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr19:38449800-38456800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:38450000-38450400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:38450000-38450400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:38450000-38450400	Enhancers	NHDF-Ad	bronchial
36	chr19:38450000-38450600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:38450000-38450600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:38450000-38450600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr19:38450000-38450800	Enhancers	Osteobl	bone
40	chr19:38450000-38452000	Weak transcription	HUVEC	blood vessel
41	chr19:38450200-38450400	Enhancers	Primary hematopoietic stem cells	blood
42	chr19:38450200-38450400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr19:38450200-38450800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr19:38450200-38451000	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr19:38450200-38453200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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