Variant report

Variant	rs2680648
Chromosome Location	chr3:53777176-53777177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11705918	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs11720848	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2253795	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2612012	0.82[CEU][hapmap]
rs2612028	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35146621	0.83[AMR][1000 genomes]
rs35447065	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774573	0.91[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs3774574	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3774583	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs3774594	0.83[AMR][1000 genomes]
rs719260	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]
rs73092085	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv520027	chr3:53762713-53784625	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2680648	IL17RB	cis	cerebellum	SCAN
rs2680648	ABHD14B	cis	parietal	SCAN
rs2680648	ACTR8	cis	parietal	SCAN
rs2680648	NPRL2	cis	parietal	SCAN
rs2680648	HEMK1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
2	chr3:53761600-53781800	Weak transcription	Spleen	Spleen
3	chr3:53764200-53779800	Weak transcription	Liver	Liver
4	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:53765000-53779800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:53765000-53779800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
8	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:53766600-53781200	Weak transcription	Lung	lung
11	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
12	chr3:53769600-53787400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:53770200-53779800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
15	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
16	chr3:53774400-53782000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:53774600-53785000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
19	chr3:53775800-53779400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:53776600-53778000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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