Variant report

Variant	rs55744465
Chromosome Location	chr2:48632455-48632456
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10169629	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208627	0.93[ASN][1000 genomes]
rs10454143	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10495951	0.87[ASN][1000 genomes]
rs10495952	0.90[ASN][1000 genomes]
rs11679523	0.90[ASN][1000 genomes]
rs11680719	0.82[EUR][1000 genomes]
rs11680916	0.90[ASN][1000 genomes]
rs11682633	0.85[ASN][1000 genomes]
rs11683099	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11685861	0.91[ASN][1000 genomes]
rs11688481	0.85[ASN][1000 genomes]
rs11689645	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11690690	0.90[ASN][1000 genomes]
rs11690748	0.90[ASN][1000 genomes]
rs11690845	0.90[ASN][1000 genomes]
rs12052754	0.88[ASN][1000 genomes]
rs12105983	0.93[ASN][1000 genomes]
rs12328506	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13398791	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13399936	0.88[EUR][1000 genomes]
rs17037289	0.90[ASN][1000 genomes]
rs17037298	0.89[ASN][1000 genomes]
rs17855177	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4344965	0.91[ASN][1000 genomes]
rs4547570	0.94[ASN][1000 genomes]
rs4638844	0.82[EUR][1000 genomes]
rs4953572	0.85[EUR][1000 genomes]
rs55660911	0.90[ASN][1000 genomes]
rs55761545	0.84[ASN][1000 genomes]
rs56156294	1.00[ASN][1000 genomes]
rs56163539	0.81[ASN][1000 genomes]
rs56365822	0.90[ASN][1000 genomes]
rs56391806	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57537506	0.89[ASN][1000 genomes]
rs57893565	0.92[ASN][1000 genomes]
rs58012056	0.91[ASN][1000 genomes]
rs58978223	0.88[ASN][1000 genomes]
rs59045263	0.93[ASN][1000 genomes]
rs60042255	0.90[ASN][1000 genomes]
rs60825643	0.94[ASN][1000 genomes]
rs61303367	0.90[ASN][1000 genomes]
rs62137015	0.91[ASN][1000 genomes]
rs62137018	0.86[ASN][1000 genomes]
rs62137019	0.90[ASN][1000 genomes]
rs62137021	0.88[ASN][1000 genomes]
rs6545036	0.83[ASN][1000 genomes]
rs66705539	0.92[ASN][1000 genomes]
rs6705802	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6718068	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6722246	0.92[ASN][1000 genomes]
rs6732196	0.82[ASN][1000 genomes]
rs6735288	0.92[ASN][1000 genomes]
rs6743757	0.90[ASN][1000 genomes]
rs6745580	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6747441	0.83[ASN][1000 genomes]
rs6749773	0.90[ASN][1000 genomes]
rs6756596	0.94[ASN][1000 genomes]
rs72818502	0.82[ASN][1000 genomes]
rs72820403	0.86[ASN][1000 genomes]
rs72820404	0.88[ASN][1000 genomes]
rs72820409	0.88[ASN][1000 genomes]
rs72820411	0.88[ASN][1000 genomes]
rs72820415	0.88[ASN][1000 genomes]
rs72820416	0.88[ASN][1000 genomes]
rs72820418	0.88[ASN][1000 genomes]
rs72820420	0.89[ASN][1000 genomes]
rs72820422	0.90[ASN][1000 genomes]
rs72820423	0.91[ASN][1000 genomes]
rs72820424	0.88[ASN][1000 genomes]
rs72820427	0.91[ASN][1000 genomes]
rs72820433	0.90[ASN][1000 genomes]
rs72820436	0.90[ASN][1000 genomes]
rs72820437	0.92[ASN][1000 genomes]
rs72820439	0.92[ASN][1000 genomes]
rs72820441	0.88[ASN][1000 genomes]
rs72820445	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820454	0.90[ASN][1000 genomes]
rs7559431	0.87[ASN][1000 genomes]
rs7562069	0.92[ASN][1000 genomes]
rs7562816	0.90[ASN][1000 genomes]
rs7566239	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7568574	0.91[ASN][1000 genomes]
rs7573316	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7576964	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7577237	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7579932	0.92[ASN][1000 genomes]
rs7600794	0.90[ASN][1000 genomes]
rs7606104	0.89[ASN][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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55744465	PPP1R21	cis	Thyroid	GTEx
rs55744465	GTF2A1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48628200-48640000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:48628600-48633600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:48632000-48634600	Enhancers	Dnd41	blood
4	chr2:48632200-48635000	Enhancers	Fetal Intestine Large	intestine
5	chr2:48632200-48635200	Enhancers	Fetal Intestine Small	intestine
6	chr2:48632400-48632600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links