Variant report

Variant	rs12609878
Chromosome Location	chr19:38882781-38882782
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	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
2	ZNF263	chr19:38882694-38883039	HEK293-T-REx	kidney:	n/a	chr19:38882859-38882880

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38879257..38881311-chr19:38881648..38883524,3	MCF-7	breast:

Variant related genes	Relation type
GGN	TF binding region
ENSG00000188766	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11083455	0.82[AMR][1000 genomes]
rs11880532	0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12608722	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2041221	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2074981	0.93[ASW][hapmap];0.90[LWK][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs2270095	0.82[CHD][hapmap]
rs2286476	0.82[CHD][hapmap]
rs3745958	0.83[EUR][1000 genomes]
rs3745959	0.83[EUR][1000 genomes]
rs57146784	0.82[EUR][1000 genomes]
rs61162240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508790	0.82[EUR][1000 genomes]
rs73044940	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12609878	ZNF221	cis	cerebellum	SCAN
rs12609878	LYPD5	cis	cerebellum	SCAN
rs12609878	SLC25A4	trans	parietal	SCAN
rs12609878	SLC1A5	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38879600-38884000	Enhancers	K562	blood
2	chr19:38880000-38885200	Weak transcription	Pancreas	Pancrea
3	chr19:38880000-38886400	Weak transcription	Gastric	stomach
4	chr19:38880200-38882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:38880200-38884400	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:38880200-38885000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:38880200-38885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:38880200-38885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:38880200-38885200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:38880200-38885400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:38880200-38887600	Weak transcription	Right Atrium	heart
12	chr19:38880400-38884000	Enhancers	A549	lung
13	chr19:38880400-38885000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:38880400-38885000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:38880600-38884000	Weak transcription	Psoas Muscle	Psoas
16	chr19:38880800-38883400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:38880800-38889200	Weak transcription	Brain Angular Gyrus	brain
18	chr19:38881000-38882800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:38881000-38883400	Weak transcription	HMEC	breast
20	chr19:38881000-38884400	Weak transcription	Brain Anterior Caudate	brain
21	chr19:38881000-38885000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr19:38881000-38885200	Weak transcription	NHEK	skin
23	chr19:38881000-38887000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr19:38881000-38887600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:38881000-38893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:38881000-38893200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:38881000-38893200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:38881000-38893200	Weak transcription	HSMMtube	muscle
29	chr19:38881200-38882800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:38881200-38887200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:38881400-38883200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr19:38881400-38883200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:38881400-38883200	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr19:38881400-38883800	Genic enhancers	NHLF	lung
35	chr19:38881600-38886200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:38881800-38882800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:38882200-38882800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
38	chr19:38882200-38883000	Bivalent Enhancer	HepG2	liver
39	chr19:38882200-38883600	Enhancers	NH-A	brain
40	chr19:38882200-38884600	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr19:38882200-38885000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:38882400-38882800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr19:38882400-38883000	Genic enhancers	H1 Cell Line	embryonic stem cell
44	chr19:38882400-38883000	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:38882400-38883000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:38882400-38883200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr19:38882400-38883200	Strong transcription	HSMM	muscle
48	chr19:38882400-38883200	Genic enhancers	HUVEC	blood vessel
49	chr19:38882400-38883600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:38882400-38883800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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