Variant report

Variant	rs9302716
Chromosome Location	chr16:59648785-59648786
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10083796	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10492918	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12709032	0.90[EUR][1000 genomes]
rs1500294	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1500295	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500297	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1566438	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1604120	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1818069	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1818071	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1827203	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202009	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202010	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2202011	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221183	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28841687	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4633709	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500043	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6500047	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198362	0.86[EUR][1000 genomes]
rs7206696	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8046365	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8052045	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054889	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8063284	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8063752	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882854	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9302715	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921279	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9922699	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926283	0.86[EUR][1000 genomes]
rs9929021	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9933491	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9934111	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9937266	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9939480	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940831	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906747	chr16:59385832-60172030	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv916423	chr16:59411801-59750824	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv572832	chr16:59578561-59756567	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv827695	chr16:59617082-59700873	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv9451	chr16:59635240-60032841	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2422221	chr16:59638102-59851643	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS 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
rs9302716	FAM54A	trans	cerebellum	SCAN
rs9302716	CES7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:59644600-59650600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:59645600-59650200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr16:59647800-59650200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr16:59648000-59648800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr16:59648600-59648800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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