Variant report

Variant	rs10880280
Chromosome Location	chr12:42667867-42667868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1069644	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10785335	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10785337	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880275	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880279	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880282	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10880284	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11181421	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1118483	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1226298	0.84[ASN][1000 genomes]
rs1238290	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12423383	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12425945	0.84[EUR][1000 genomes]
rs17091052	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1826387	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1961953	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2061191	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061192	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085314	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2100547	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2198763	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761677	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4402364	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4417370	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768397	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768398	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6582385	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6582389	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6582392	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712108	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs712109	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs712112	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs712114	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs712115	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs712118	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs712120	0.92[ASN][1000 genomes]
rs712122	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs712123	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs712125	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs712129	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7298965	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302687	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7316575	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7486516	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7956016	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7959339	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7960176	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7970115	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs824738	0.80[ASN][1000 genomes]
rs824739	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs824741	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs866091	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv826351	chr12:42584218-42676281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv826352	chr12:42593124-42675255	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880280	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42667400-42668000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:42667600-42668000	Weak transcription	Pancreas	Pancrea
3	chr12:42667800-42668000	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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