Variant report

Variant	rs1582588
Chromosome Location	chr16:59373755-59373756
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1019571	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1022099	0.89[EUR][1000 genomes]
rs1027913	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10431930	0.89[EUR][1000 genomes]
rs12447529	0.86[EUR][1000 genomes]
rs12709025	0.96[EUR][1000 genomes]
rs12925044	0.95[EUR][1000 genomes]
rs12928697	0.85[EUR][1000 genomes]
rs12929739	0.86[EUR][1000 genomes]
rs1303842	0.86[EUR][1000 genomes]
rs1423982	0.87[TSI][hapmap]
rs1580380	0.85[TSI][hapmap]
rs1593112	0.95[EUR][1000 genomes]
rs1593146	0.86[EUR][1000 genomes]
rs1593148	0.86[EUR][1000 genomes]
rs1610077	0.95[EUR][1000 genomes]
rs1813437	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1828343	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1834058	0.96[EUR][1000 genomes]
rs1834064	0.84[EUR][1000 genomes]
rs2036805	0.95[EUR][1000 genomes]
rs2036806	0.94[EUR][1000 genomes]
rs2036807	0.87[EUR][1000 genomes]
rs2081226	0.89[EUR][1000 genomes]
rs2081227	0.89[EUR][1000 genomes]
rs2089727	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2098731	0.89[EUR][1000 genomes]
rs2406766	0.86[EUR][1000 genomes]
rs2406779	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3958621	0.94[EUR][1000 genomes]
rs4146209	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4784076	0.89[EUR][1000 genomes]
rs4785028	0.95[EUR][1000 genomes]
rs4785029	0.95[EUR][1000 genomes]
rs4785030	0.86[EUR][1000 genomes]
rs4785034	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6500029	0.86[EUR][1000 genomes]
rs6500031	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6500033	0.81[EUR][1000 genomes]
rs7195264	0.89[EUR][1000 genomes]
rs7198374	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7198887	0.94[EUR][1000 genomes]
rs7201230	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7202206	0.81[EUR][1000 genomes]
rs7202693	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204255	0.93[EUR][1000 genomes]
rs8043584	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8056029	0.89[EUR][1000 genomes]
rs907053	0.86[EUR][1000 genomes]
rs9927205	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9927985	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833249	chr16:59282950-59461023	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv906745	chr16:59323025-59408342	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv906746	chr16:59323025-59423982	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1582588	MT1F	cis	cerebellum	SCAN
rs1582588	NUDT21	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:59373000-59373800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:59373400-59375400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr16:59373600-59374400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:59373600-59374600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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