Variant report

Variant	rs12475386
Chromosome Location	chr2:40094081-40094082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10188106	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11692413	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11695763	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13424439	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541564	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17480505	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1861248	1.00[ASN][1000 genomes]
rs2080296	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2192703	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373702	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55768815	0.96[ASN][1000 genomes]
rs60399093	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137179	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62137180	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62137182	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62137183	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137185	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137188	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137214	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6732387	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7556977	0.96[ASN][1000 genomes]
rs7562741	0.91[ASN][1000 genomes]
rs887994	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003593	chr2:40009597-40165666	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535651	chr2:40009597-40165666	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv873891	chr2:40046658-40173905	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv430947	chr2:40080723-40141649	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv581496	chr2:40082054-40123904	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1003896	chr2:40094081-40231585	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12475386	PLEKHH2	cis	cerebellum	SCAN
rs12475386	SRSF7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40093200-40097200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:40093600-40097200	Weak transcription	HMEC	breast
3	chr2:40094000-40098400	Weak transcription	Dnd41	blood

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