Variant report

Variant	rs1852686
Chromosome Location	chr2:145809250-145809251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10206585	0.86[EUR][1000 genomes]
rs10209654	0.88[AFR][1000 genomes]
rs10928241	0.86[EUR][1000 genomes]
rs12474485	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12476764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995180	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13384504	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1819055	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830318	0.83[AMR][1000 genomes]
rs1830320	0.86[EUR][1000 genomes]
rs1852687	0.83[AFR][1000 genomes]
rs1881409	0.83[AMR][1000 genomes]
rs1976974	0.80[AFR][1000 genomes]
rs2252383	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252654	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34372836	0.85[EUR][1000 genomes]
rs6747171	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6749506	0.86[EUR][1000 genomes]
rs7423637	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7592365	0.87[AFR][1000 genomes]
rs7604735	0.85[EUR][1000 genomes]
rs7607110	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957293	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

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	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv932113	chr2:145515124-145844491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv834398	chr2:145659419-145830156	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv431768	chr2:145741527-145981491	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1852686	PTPDC1	trans	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145803000-145815800	Weak transcription	NHDF-Ad	bronchial
2	chr2:145806200-145810400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:145806600-145809400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:145807800-145810400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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