Variant report

Variant	rs4803675
Chromosome Location	chr19:44589716-44589717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44589107..44593140-chr19:44596665..44599244,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267680	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs12232810	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1996408	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2191566	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2270196	0.86[JPT][hapmap]
rs2356549	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs367209	0.86[JPT][hapmap]
rs369106	0.86[JPT][hapmap]
rs3810406	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs390369	0.86[JPT][hapmap]
rs4433920	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4482396	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803667	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4803669	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4803673	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55771992	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55812285	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56149185	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56182773	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56317065	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56320525	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62115482	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62115484	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62115489	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62115511	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62115513	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62119176	0.81[AMR][1000 genomes]
rs6509138	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7245749	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7254261	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7254907	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7255315	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7255512	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7255701	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7256908	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7258517	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7260075	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73037629	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8104437	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104605	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104802	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105315	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105571	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs8105574	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv978827	chr19:44584843-44590122	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4803675	APOC4	cis	parietal	SCAN
rs4803675	PTGIR	cis	cerebellum	SCAN
rs4803675	ZNF155	cis	multi-tissue	Pritchard
rs4803675	CCDC114	cis	cerebellum	SCAN
rs4803675	OPA3	cis	parietal	SCAN
rs4803675	HIF3A	cis	parietal	SCAN
rs4803675	FOXA3	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44577000-44598000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44577200-44590000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:44577200-44598000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:44577600-44589800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:44577600-44597800	Weak transcription	HMEC	breast
6	chr19:44580600-44591400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:44580600-44592400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:44580600-44592600	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:44580800-44593200	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:44581000-44591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:44581000-44591400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:44581000-44591800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:44581200-44591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:44581200-44591600	Strong transcription	Dnd41	blood
15	chr19:44581200-44592400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:44581200-44593000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:44581400-44591000	Strong transcription	Fetal Intestine Large	intestine
18	chr19:44581600-44590000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:44581800-44592000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:44581800-44592800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:44582000-44591400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:44582000-44592600	Strong transcription	Fetal Stomach	stomach
23	chr19:44582200-44592800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:44582800-44591400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:44583000-44591600	Strong transcription	Primary T cells from cord blood	blood
26	chr19:44583200-44593000	Strong transcription	Fetal Brain Female	brain
27	chr19:44583400-44591800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr19:44583600-44593200	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:44583800-44591600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr19:44584000-44591400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:44584000-44592800	ZNF genes & repeats	Liver	Liver
32	chr19:44584000-44593400	Strong transcription	Adipose Nuclei	Adipose
33	chr19:44584200-44590800	Strong transcription	Colon Smooth Muscle	Colon
34	chr19:44584200-44591200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr19:44584200-44591200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:44584200-44591200	Strong transcription	Spleen	Spleen
37	chr19:44584200-44591400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:44584200-44591400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:44584200-44591400	Strong transcription	Brain Germinal Matrix	brain
40	chr19:44584200-44591400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr19:44584200-44591400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr19:44584200-44591800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:44584200-44592400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:44584200-44592800	Strong transcription	Left Ventricle	heart
45	chr19:44584200-44593400	Strong transcription	Fetal Lung	lung
46	chr19:44584200-44593400	Strong transcription	Ovary	ovary
47	chr19:44584400-44590000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:44584800-44590400	Strong transcription	Brain Substantia Nigra	brain
49	chr19:44584800-44591200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:44584800-44591200	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links