Variant report

Variant	rs739461
Chromosome Location	chr19:19715794-19715795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19706085..19710226-chr19:19714067..19716882,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10403759	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878202	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11879838	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12976826	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16994684	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16996174	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1968047	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2043293	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2304129	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34725331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808974	0.98[ASN][1000 genomes]
rs7252228	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8101679	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113682	0.95[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880090	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv518076	chr19:19692579-19715794	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs739461	GATAD2A	cis	parietal	SCAN
rs739461	MED26	cis	parietal	SCAN
rs739461	IL12RB1	cis	parietal	SCAN
rs739461	OR10H4	cis	parietal	SCAN
rs739461	OCEL1	cis	parietal	SCAN
rs739461	UNC13A	cis	cerebellum	SCAN
rs739461	DDX49	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19702600-19719400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19703400-19717000	Weak transcription	Fetal Muscle Leg	muscle
3	chr19:19703800-19717000	Weak transcription	Spleen	Spleen
4	chr19:19706600-19717000	Weak transcription	Esophagus	oesophagus
5	chr19:19706600-19728200	Weak transcription	Fetal Brain Male	brain
6	chr19:19707000-19718600	Weak transcription	Fetal Lung	lung
7	chr19:19707200-19717000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr19:19707400-19716800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:19707600-19716800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:19707600-19728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:19707800-19716800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:19708000-19716800	Enhancers	Fetal Thymus	thymus
13	chr19:19708800-19716800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr19:19708800-19720000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:19708800-19724400	Weak transcription	NHDF-Ad	bronchial
16	chr19:19709000-19719200	Weak transcription	Fetal Brain Female	brain
17	chr19:19710200-19716800	Weak transcription	Dnd41	blood
18	chr19:19710200-19718800	Weak transcription	Fetal Stomach	stomach
19	chr19:19712800-19719400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:19712800-19724400	Weak transcription	Gastric	stomach
21	chr19:19713200-19719400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr19:19713400-19717000	Weak transcription	Placenta	Placenta
23	chr19:19713600-19716600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr19:19713600-19716800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr19:19713600-19718600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:19713800-19716800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr19:19713800-19718400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:19713800-19719200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:19713800-19728000	Weak transcription	Brain Germinal Matrix	brain
30	chr19:19714000-19716800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:19714000-19716800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:19714000-19716800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr19:19714000-19716800	Weak transcription	GM12878-XiMat	blood
34	chr19:19714000-19717000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:19714000-19717000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:19714000-19717000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:19714000-19717200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:19714000-19728800	Weak transcription	Brain Anterior Caudate	brain
39	chr19:19714200-19716400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr19:19714200-19716800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr19:19714200-19716800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:19714200-19716800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr19:19714200-19724400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:19714400-19716400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:19714400-19716800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:19714400-19716800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:19714400-19717000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:19714600-19716400	Weak transcription	Stomach Mucosa	stomach
49	chr19:19714600-19716400	Weak transcription	Thymus	Thymus
50	chr19:19714600-19716400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links