Variant report

Variant	rs1860325
Chromosome Location	chr19:55612969-55612970
allele	G/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	POLR2A	chr19:55612833-55613076	K562	blood:	n/a	n/a
2	USF1	chr19:55612711-55612979	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55611452..55618868-chr19:55626160..55631612,12	K562	blood:
2	chr19:55610882..55614666-chr19:55626430..55628703,3	MCF-7	breast:
3	chr19:55609257..55613232-chr19:55613674..55618222,6	K562	blood:

Variant related genes	Relation type
PPP1R12C	TF binding region
ENSG00000125503	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10404178	1.00[CHD][hapmap]
rs2603697	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs575144	0.92[CEU][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs667451	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv1063666	chr19:55030439-55622780	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv817874	chr19:55595687-55614923	Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv912449	chr19:55595687-55630425	Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv912450	chr19:55595687-55633043	Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv912452	chr19:55595687-55644325	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1860325	EPS8L1	cis	Artery Tibial	GTEx
rs1860325	RDH13	cis	Artery Aorta	GTEx
rs1860325	RDH13	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55593800-55620400	Weak transcription	HMEC	breast
2	chr19:55599200-55626600	Weak transcription	Fetal Kidney	kidney
3	chr19:55599200-55627200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:55599400-55614800	Weak transcription	GM12878-XiMat	blood
5	chr19:55599800-55626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:55600000-55613400	Weak transcription	Fetal Lung	lung
7	chr19:55600000-55613800	Weak transcription	NH-A	brain
8	chr19:55600000-55614600	Weak transcription	HSMM	muscle
9	chr19:55600000-55626600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:55600000-55627000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:55600200-55614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:55600600-55614600	Weak transcription	HUVEC	blood vessel
13	chr19:55601400-55626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:55602000-55613800	Strong transcription	Gastric	stomach
15	chr19:55602000-55615400	Strong transcription	Lung	lung
16	chr19:55602000-55618400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:55602800-55614200	Weak transcription	Psoas Muscle	Psoas
18	chr19:55602800-55626400	Weak transcription	Hela-S3	cervix
19	chr19:55605600-55614400	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:55606400-55613600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:55606400-55613800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:55606400-55621600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:55606600-55614000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:55606600-55614200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:55606600-55627200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:55606800-55613200	Weak transcription	Brain Angular Gyrus	brain
27	chr19:55606800-55613800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:55607000-55613600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:55607000-55614800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:55607200-55613000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:55607200-55613400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr19:55607600-55624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:55607800-55614800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:55609000-55613800	Strong transcription	Pancreas	Pancrea
35	chr19:55609000-55614200	Strong transcription	Fetal Stomach	stomach
36	chr19:55609000-55614400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:55609000-55614600	Strong transcription	Adipose Nuclei	Adipose
38	chr19:55609000-55614800	Strong transcription	Esophagus	oesophagus
39	chr19:55609000-55616000	Strong transcription	Colon Smooth Muscle	Colon
40	chr19:55609000-55618400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:55609200-55614000	Strong transcription	Fetal Brain Female	brain
42	chr19:55609200-55615000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr19:55609200-55615200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:55609200-55615200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:55609400-55614400	Strong transcription	Fetal Intestine Small	intestine
46	chr19:55609400-55614600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:55609400-55614600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr19:55609400-55614600	Strong transcription	Fetal Intestine Large	intestine
49	chr19:55609400-55614600	Strong transcription	Thymus	Thymus
50	chr19:55609400-55614800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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