Variant report

Variant	rs10880279
Chromosome Location	chr12:42664105-42664106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42630764..42634412-chr12:42661858..42664112,3	K562	blood:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1043652	0.96[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs1043656	0.96[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs1069644	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10785335	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785337	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880280	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880282	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10880284	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs11181421	0.82[EUR][1000 genomes]
rs11181427	0.80[EUR][1000 genomes]
rs11181461	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs1118483	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12229266	0.96[CEU][hapmap]
rs12231335	0.95[CEU][hapmap]
rs1226298	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1226303	0.88[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap]
rs1238290	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12423383	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs12425945	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs12578312	0.92[CEU][hapmap]
rs1376931	0.92[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs1463613	0.93[JPT][hapmap]
rs1628871	0.92[JPT][hapmap]
rs1669884	0.92[CEU][hapmap]
rs1669903	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1669937	0.92[CEU][hapmap]
rs1683195	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs17091052	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1732351	0.85[GIH][hapmap];0.87[JPT][hapmap]
rs1732352	0.87[JPT][hapmap]
rs1796357	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1796389	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1796392	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1796398	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1826387	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1961953	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2061191	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2061192	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2085314	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2100547	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2198763	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243465	0.92[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs2605401	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3213989	0.88[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs3761677	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs3827524	0.92[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs4402364	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417370	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768397	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4768398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4768401	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs6582378	0.83[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap]
rs6582385	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6582386	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6582389	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6582392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712106	0.93[JPT][hapmap]
rs712108	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712109	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs712112	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs712114	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712115	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712118	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs712119	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs712120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs712122	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712123	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712125	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs712126	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs712127	0.82[AMR][1000 genomes]
rs712129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7134895	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7298965	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302687	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7303028	0.86[GIH][hapmap]
rs7316575	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7486516	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7956016	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959339	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7960176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7975518	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7978993	0.87[JPT][hapmap]
rs824716	0.87[JPT][hapmap]
rs824724	0.87[JPT][hapmap]
rs824734	0.88[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap]
rs824738	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs824739	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs824741	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs844046	0.93[JPT][hapmap]
rs865420	0.88[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs866091	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs896555	0.92[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv3397788	chr12:42636734-42665519	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10880279	PPHLN1	cis	Artery Tibial	GTEx
rs10880279	PPHLN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42659600-42667800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:42662000-42667400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:42664000-42665800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links