Variant report

Variant	rs17607383
Chromosome Location	chr1:76512161-76512162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10443175	0.80[EUR][1000 genomes]
rs10873865	0.90[EUR][1000 genomes]
rs12123144	0.91[CEU][hapmap]
rs12123760	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs12125940	0.83[EUR][1000 genomes]
rs12126074	0.83[EUR][1000 genomes]
rs12143779	1.00[LWK][hapmap]
rs12145522	0.83[EUR][1000 genomes]
rs1251484	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1251485	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1251486	0.94[EUR][1000 genomes]
rs1251489	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1251492	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1251494	0.95[EUR][1000 genomes]
rs1251495	0.95[EUR][1000 genomes]
rs1251496	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1251501	0.94[EUR][1000 genomes]
rs1251502	0.94[EUR][1000 genomes]
rs1251504	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1251505	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1251506	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1251507	0.94[EUR][1000 genomes]
rs1251509	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1251510	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1251511	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1251512	0.94[EUR][1000 genomes]
rs1251513	0.94[EUR][1000 genomes]
rs1266117	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1340690	0.89[EUR][1000 genomes]
rs1340691	0.86[EUR][1000 genomes]
rs17659615	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770895	0.86[EUR][1000 genomes]
rs1889751	1.00[LWK][hapmap]
rs34354538	0.84[EUR][1000 genomes]
rs35318380	0.83[EUR][1000 genomes]
rs35381129	0.83[EUR][1000 genomes]
rs5022490	0.94[EUR][1000 genomes]
rs60182743	0.83[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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2754129	chr1:76489579-76529279	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17607383	MSH4	cis	parietal	SCAN
rs17607383	ACADM	cis	cerebellum	SCAN
rs17607383	SNORD45B	cis	cerebellum	SCAN
rs17607383	NEGR1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76506400-76514000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:76506600-76514000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:76507600-76513600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:76507800-76513800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:76507800-76514000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:76509800-76514000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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