Variant report

Variant	rs168506
Chromosome Location	chr2:54919899-54919900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10180713	0.91[CEU][hapmap]
rs10191922	0.96[ASN][1000 genomes]
rs1047499	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs11892788	0.86[CEU][hapmap]
rs12105792	1.00[ASW][hapmap];0.81[MKK][hapmap]
rs12467581	0.82[EUR][1000 genomes]
rs13016942	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap]
rs1541854	0.81[EUR][1000 genomes]
rs168503	0.85[ASN][1000 genomes]
rs171350	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17344072	0.82[CEU][hapmap]
rs181348	0.81[ASN][1000 genomes]
rs1821138	0.86[ASN][1000 genomes]
rs1864493	0.82[CEU][hapmap]
rs187124	0.90[ASN][1000 genomes]
rs191628	0.85[ASN][1000 genomes]
rs2292356	0.83[EUR][1000 genomes]
rs2567835	0.88[ASN][1000 genomes]
rs2931463	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2931464	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2941584	0.87[CHB][hapmap];0.82[MEX][hapmap]
rs2941586	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2941587	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2941591	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2941595	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2971874	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2971875	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2971877	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2971879	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2971883	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2971887	0.81[EUR][1000 genomes]
rs2971889	0.82[ASN][1000 genomes]
rs354187	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs354209	0.88[ASN][1000 genomes]
rs354213	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs354214	0.88[ASN][1000 genomes]
rs354223	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs354224	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs354226	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs354228	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs354231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs354236	0.91[CHB][hapmap];0.81[MKK][hapmap]
rs354237	0.91[CHB][hapmap]
rs354238	0.91[CHB][hapmap]
rs354243	0.85[ASN][1000 genomes]
rs3796014	0.81[EUR][1000 genomes]
rs4444573	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4519562	0.82[EUR][1000 genomes]
rs4671226	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs4671951	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap]
rs4671956	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[LWK][hapmap]
rs4671961	0.81[CHD][hapmap]
rs6545419	0.82[CEU][hapmap]
rs6545429	0.80[CEU][hapmap]
rs6545434	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6706372	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6731661	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs6732949	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6734658	0.81[EUR][1000 genomes]
rs6748816	0.82[EUR][1000 genomes]
rs6761398	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs7607451	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs907135	0.91[CEU][hapmap]

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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv963149	chr2:54914350-54920863	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs168506	SPTBN1	cis	cerebellum	SCAN
rs168506	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54908800-54921400	Weak transcription	Lung	lung
2	chr2:54919400-54922400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:54919400-54924800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:54919600-54921200	Weak transcription	HepG2	liver
5	chr2:54919600-54921400	Weak transcription	Fetal Intestine Large	intestine
6	chr2:54919800-54922800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54919800-54925600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links