Variant report

Variant	rs719260
Chromosome Location	chr3:53789172-53789173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11705918	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11720848	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2253795	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2612012	0.87[CEU][hapmap]
rs2612028	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2680648	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35146621	0.87[AMR][1000 genomes]
rs35447065	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3774573	0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs3774574	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3774583	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs3774594	0.84[AMR][1000 genomes]
rs3774595	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs73092085	0.86[EUR][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs719260	HEMK1	cis	cerebellum	SCAN
rs719260	IL17RB	cis	cerebellum	SCAN
rs719260	ACTR8	cis	parietal	SCAN
rs719260	NPRL2	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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