Variant report

Variant	rs12613732
Chromosome Location	chr2:31249427-31249428
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31247169..31249491-chr2:31252132..31255050,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10198054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10209881	0.96[MEX][hapmap]
rs10865086	0.81[AMR][1000 genomes]
rs12464083	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12617279	0.86[CEU][hapmap]
rs12621546	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12621813	0.81[ASN][1000 genomes]
rs12712300	0.88[MEX][hapmap]
rs12712301	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12712304	0.91[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12999804	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009779	0.82[CEU][hapmap]
rs1862966	0.87[MEX][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs1862967	0.91[MEX][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs1862968	0.81[YRI][hapmap];0.81[AMR][1000 genomes]
rs2194455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4245766	0.82[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs4951960	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4952028	0.83[CHB][hapmap]
rs5009910	0.92[MEX][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs6752303	0.92[MEX][hapmap]
rs7558425	0.83[AMR][1000 genomes]
rs7605643	0.88[MEX][hapmap]
rs7605982	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608731	0.92[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12613732	PLLP	trans	cerebellum	SCAN
rs12613732	SLC30A6	cis	cerebellum	SCAN
rs12613732	FAM179A	cis	cerebellum	SCAN
rs12613732	GALNT14	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31232600-31251000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:31235200-31251000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:31235400-31251000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:31246400-31251000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:31246400-31261600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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