Variant report

Variant	rs714786
Chromosome Location	chr3:53789022-53789023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11719163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918583	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28365115	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28434705	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733070	0.83[EUR][1000 genomes]
rs3774558	0.83[AMR][1000 genomes]
rs3774567	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3774570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774577	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs3774580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821860	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3821866	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3846215	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276449	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56384446	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6776947	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797014	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311514	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809645	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs714786	ACTR8	cis	parietal	SCAN
rs714786	PDE12	cis	parietal	SCAN
rs714786	RBM5	cis	parietal	SCAN
rs714786	NPRL2	cis	parietal	SCAN
rs714786	RPL29	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
2	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
4	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
5	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:53778800-53797000	Weak transcription	Pancreas	Pancrea
7	chr3:53779000-53806400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:53780400-53807000	Weak transcription	Fetal Brain Female	brain
9	chr3:53781800-53807400	Weak transcription	Brain Anterior Caudate	brain
10	chr3:53783800-53790000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:53785000-53811200	Weak transcription	Spleen	Spleen
12	chr3:53785400-53795400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:53785800-53806600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:53786000-53795600	Weak transcription	Brain Angular Gyrus	brain
15	chr3:53786000-53808200	Weak transcription	Liver	Liver
16	chr3:53787000-53790000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:53787200-53789200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:53787200-53789600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:53787800-53792800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:53788200-53797400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:53788600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:53788600-53789400	Strong transcription	Fetal Kidney	kidney
23	chr3:53788600-53795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:53788800-53789200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:53788800-53795200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:53788800-53798400	Weak transcription	Lung	lung
27	chr3:53788800-53807000	Weak transcription	Brain Inferior Temporal Lobe	brain

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