Variant report

Variant	rs6800641
Chromosome Location	chr3:53770588-53770589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1020822	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10510765	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11130380	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11705918	0.86[CEU][hapmap]
rs11708227	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11708934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709505	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11719179	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13075639	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs13076366	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs13092344	0.84[EUR][1000 genomes]
rs17053382	0.86[ASN][1000 genomes]
rs17053417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029331	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070616	0.93[ASN][1000 genomes]
rs2125876	0.86[EUR][1000 genomes]
rs2248381	0.93[ASN][1000 genomes]
rs2306865	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2306866	0.91[ASN][1000 genomes]
rs2359204	0.86[EUR][1000 genomes]
rs2362424	0.82[ASN][1000 genomes]
rs2612012	0.82[CEU][hapmap]
rs2633723	0.93[ASN][1000 genomes]
rs28675949	0.82[EUR][1000 genomes]
rs35377175	0.84[EUR][1000 genomes]
rs35414202	0.84[EUR][1000 genomes]
rs35657034	0.82[EUR][1000 genomes]
rs3796346	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4453827	0.86[EUR][1000 genomes]
rs62253777	0.93[ASN][1000 genomes]
rs62253778	0.98[ASN][1000 genomes]
rs723540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628839	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs898423	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1000280	chr3:53742736-53770588	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
rs6800641	HEMK1	cis	cerebellum	SCAN
rs6800641	SEMA3G	cis	parietal	SCAN
rs6800641	CCDC66	cis	parietal	SCAN
rs6800641	FAM116A	cis	cerebellum	SCAN
rs6800641	IL17RB	cis	cerebellum	SCAN

Chromatin state (count:18 , 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	chr3:53764600-53770800	Strong transcription	Fetal Intestine Large	intestine
5	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:53765000-53773600	Weak transcription	Fetal Brain Male	brain
7	chr3:53765000-53779800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:53765000-53779800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
10	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
11	chr3:53765400-53774000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:53766600-53781200	Weak transcription	Lung	lung
14	chr3:53768400-53774000	Strong transcription	Fetal Intestine Small	intestine
15	chr3:53768600-53770600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
17	chr3:53769600-53787400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:53770200-53779800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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