Variant report

Variant	rs2840319
Chromosome Location	chr1:85886224-85886225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10747318	0.83[AFR][1000 genomes]
rs10782549	0.86[AFR][1000 genomes]
rs10873701	0.83[AFR][1000 genomes]
rs10873702	0.93[AFR][1000 genomes]
rs11161606	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161607	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11161611	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1146374	0.81[AFR][1000 genomes]
rs12047422	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12140103	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1357635	0.85[AFR][1000 genomes]
rs1523994	0.83[AFR][1000 genomes]
rs1523995	0.83[AFR][1000 genomes]
rs1554597	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1608537	0.86[AFR][1000 genomes]
rs1884139	0.85[AMR][1000 genomes]
rs1965876	0.86[AFR][1000 genomes]
rs1975755	0.86[AFR][1000 genomes]
rs2011825	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2012683	0.84[AMR][1000 genomes]
rs2016104	0.85[AFR][1000 genomes]
rs2177461	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2207368	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs233047	0.81[AMR][1000 genomes]
rs233050	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs233054	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs233091	0.80[AMR][1000 genomes]
rs233093	0.80[AMR][1000 genomes]
rs233099	0.81[AMR][1000 genomes]
rs2474123	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2892888	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3920521	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3949301	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4949900	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58821561	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6420965	0.84[AFR][1000 genomes]
rs6576761	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6576764	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6576767	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6657817	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6671599	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6704103	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67611930	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72724606	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs729655	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515261	0.83[AFR][1000 genomes]
rs7525786	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7539738	0.81[AFR][1000 genomes]
rs7546931	0.92[AFR][1000 genomes]
rs7547571	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997251	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85873800-85887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:85874000-85903800	Weak transcription	NHLF	lung
3	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:85874400-85903600	Weak transcription	HepG2	liver
5	chr1:85874400-85904200	Weak transcription	NH-A	brain
6	chr1:85880400-85887600	Weak transcription	Osteobl	bone
7	chr1:85883200-85887000	Weak transcription	HSMM	muscle
8	chr1:85883200-85893400	Weak transcription	Aorta	Aorta
9	chr1:85884800-85886800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:85885000-85886400	ZNF genes & repeats	Fetal Intestine Large	intestine
11	chr1:85885000-85886800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:85885000-85889400	Weak transcription	HUVEC	blood vessel
13	chr1:85885400-85886800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:85885600-85886400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
15	chr1:85885600-85886400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:85885600-85886800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:85885800-85886400	ZNF genes & repeats	HSMMtube	muscle
18	chr1:85886000-85887600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:85886200-85886400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links