Variant report

Variant	rs4147482
Chromosome Location	chr1:166087621-166087622
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	chr1:166083108..166085855-chr1:166087438..166089493,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1002160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10753704	0.89[EUR][1000 genomes]
rs10753709	0.86[GIH][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10753710	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10800183	0.88[CEU][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs10800184	0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs10800186	0.89[EUR][1000 genomes]
rs10800187	0.90[EUR][1000 genomes]
rs10800191	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10800192	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10800193	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10918344	0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs10918345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10918347	0.86[EUR][1000 genomes]
rs10918348	0.90[EUR][1000 genomes]
rs10918349	0.90[EUR][1000 genomes]
rs10918362	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10918367	0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10918368	0.87[GIH][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10918370	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10918372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10918373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10918375	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11487531	0.90[EUR][1000 genomes]
rs11590461	0.90[EUR][1000 genomes]
rs12030010	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12078862	0.83[EUR][1000 genomes]
rs12090916	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12097635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12123839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132672	0.84[EUR][1000 genomes]
rs12145793	0.85[EUR][1000 genomes]
rs12756802	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs28718625	0.90[EUR][1000 genomes]
rs34402000	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4072242	0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4147071	0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs4339838	0.87[GIH][hapmap];0.92[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4542195	0.87[GIH][hapmap];0.88[LWK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4657520	0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs4657522	0.92[EUR][1000 genomes]
rs55704823	0.90[EUR][1000 genomes]
rs56044172	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59317225	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59384574	0.90[EUR][1000 genomes]
rs6426970	0.93[EUR][1000 genomes]
rs6659245	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664520	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6692196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700318	0.92[EUR][1000 genomes]
rs6700427	0.90[EUR][1000 genomes]
rs72703921	0.88[EUR][1000 genomes]
rs731264	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7521995	0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7530896	0.93[EUR][1000 genomes]
rs7553768	0.93[EUR][1000 genomes]
rs919674	0.96[TSI][hapmap];0.93[EUR][1000 genomes]

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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4147482	PVRL4	cis	cerebellum	SCAN
rs4147482	CD48	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166080800-166104200	Weak transcription	Pancreas	Pancrea
2	chr1:166083000-166110800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:166085400-166093200	Weak transcription	Spleen	Spleen
4	chr1:166087200-166089200	Enhancers	H9 Cell Line	embryonic stem cell

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