Variant report

Variant	rs3116406
Chromosome Location	chr1:84874242-84874243
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10493746	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874441	0.91[ASN][1000 genomes]
rs12755232	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1340598	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1506702	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1506703	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17131698	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17131701	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17131702	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17131707	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1827939	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1911156	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1959757	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1959758	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2008711	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2105267	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2389742	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34519183	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35779335	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738573	0.84[JPT][hapmap]
rs3768250	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768256	0.84[JPT][hapmap]
rs4345821	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4907066	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61766293	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61766294	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs633294	0.84[JPT][hapmap]
rs634531	0.89[JPT][hapmap]
rs6701340	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514800	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538902	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549128	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959363	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84871000-84874400	Enhancers	Fetal Intestine Large	intestine
2	chr1:84871200-84874400	Enhancers	Fetal Intestine Small	intestine
3	chr1:84872000-84874400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:84872000-84876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:84872200-84874400	Enhancers	Stomach Mucosa	stomach
6	chr1:84872400-84875000	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:84872400-84876800	Weak transcription	Gastric	stomach
8	chr1:84873200-84876400	Weak transcription	Osteobl	bone
9	chr1:84873400-84874400	Enhancers	Liver	Liver
10	chr1:84874000-84876000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:84874000-84876000	Weak transcription	HUVEC	blood vessel
12	chr1:84874000-84878200	Weak transcription	Psoas Muscle	Psoas
13	chr1:84874200-84875200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:84874200-84875200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:84874200-84875400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:84874200-84875600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:84874200-84876200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:84874200-84876400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:84874200-84878000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:84874200-84878200	Weak transcription	Muscle Satellite Cultured Cells	--

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