Variant report

Variant	rs12119958
Chromosome Location	chr1:71703438-71703439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTH-6	chr1:71702813-71703799	NONHSAT003893

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1009311	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10493481	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11209743	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11209745	0.94[JPT][hapmap]
rs11209747	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11209756	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209757	0.93[ASN][1000 genomes]
rs11209761	0.87[ASN][1000 genomes]
rs11209762	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11811835	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12084460	0.94[JPT][hapmap]
rs12118599	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12131265	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12139565	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140289	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12729268	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12737582	0.87[ASN][1000 genomes]
rs12744775	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12748649	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1367767	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1395289	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1418449	0.92[ASN][1000 genomes]
rs1546809	1.00[ASN][1000 genomes]
rs1573061	0.96[ASN][1000 genomes]
rs1832900	0.90[ASN][1000 genomes]
rs1954285	0.96[ASN][1000 genomes]
rs2066371	0.96[ASN][1000 genomes]
rs2066373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639329	0.96[ASN][1000 genomes]
rs2639330	1.00[ASN][1000 genomes]
rs2639331	0.95[ASN][1000 genomes]
rs2639335	0.96[ASN][1000 genomes]
rs2639338	0.96[ASN][1000 genomes]
rs2694954	1.00[ASN][1000 genomes]
rs2790675	1.00[ASN][1000 genomes]
rs2796187	0.98[ASN][1000 genomes]
rs2796188	0.98[ASN][1000 genomes]
rs2796189	0.98[ASN][1000 genomes]
rs2796190	0.98[ASN][1000 genomes]
rs2796192	1.00[ASN][1000 genomes]
rs2796196	0.88[ASN][1000 genomes]
rs2796199	0.94[JPT][hapmap]
rs2796201	0.96[ASN][1000 genomes]
rs2796202	0.96[ASN][1000 genomes]
rs2796203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2817869	1.00[JPT][hapmap]
rs4128461	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs4272572	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4367753	0.88[ASN][1000 genomes]
rs4397614	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4425938	0.96[ASN][1000 genomes]
rs4520371	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs4650099	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4650100	0.96[CEU][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs6680193	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7411	1.00[JPT][hapmap]
rs7516464	0.94[JPT][hapmap]
rs7519104	0.94[JPT][hapmap]
rs7525499	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556111	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs880098	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs952337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1005726	chr1:71701840-71953242	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12119958	PTGER3	cis	Skin Sun Exposed Lower leg	GTEx
rs12119958	PTGER3	cis	uninvolved skin	skin_eQTL

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links