Variant report

Variant	rs1251507
Chromosome Location	chr1:76525783-76525784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10443175	0.83[EUR][1000 genomes]
rs10782605	0.81[EUR][1000 genomes]
rs10873865	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12123144	0.95[CEU][hapmap]
rs12123760	0.95[CEU][hapmap]
rs12125940	0.83[EUR][1000 genomes]
rs12126074	0.83[EUR][1000 genomes]
rs12145522	0.83[EUR][1000 genomes]
rs1251467	0.92[CHD][hapmap]
rs1251484	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1251485	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1251486	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251489	0.99[EUR][1000 genomes]
rs1251492	0.98[EUR][1000 genomes]
rs1251494	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251495	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251496	0.98[EUR][1000 genomes]
rs1251501	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1251502	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1251504	0.98[EUR][1000 genomes]
rs1251505	0.98[EUR][1000 genomes]
rs1251506	0.98[EUR][1000 genomes]
rs1251509	0.99[EUR][1000 genomes]
rs1251510	0.97[EUR][1000 genomes]
rs1251511	0.98[EUR][1000 genomes]
rs1251512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251513	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1266117	0.98[EUR][1000 genomes]
rs1340690	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1340691	0.86[EUR][1000 genomes]
rs17607383	0.94[EUR][1000 genomes]
rs17659615	0.93[EUR][1000 genomes]
rs1770895	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34354538	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35318380	0.83[EUR][1000 genomes]
rs35381129	0.83[EUR][1000 genomes]
rs5022490	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60182743	0.83[EUR][1000 genomes]
rs7545219	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv947186	chr1:76512447-76530843	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1477	chr1:76515963-76534339	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv521786	chr1:76525783-76535434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1251507	ACADM	cis	cerebellum	SCAN
rs1251507	NEGR1	cis	parietal	SCAN
rs1251507	MSH4	cis	parietal	SCAN
rs1251507	SNORD45B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76521800-76531000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:76524400-76526200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:76524600-76526000	Enhancers	Brain Substantia Nigra	brain
4	chr1:76524800-76525800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:76524800-76526200	Enhancers	A549	lung
6	chr1:76525600-76527600	Weak transcription	Brain Germinal Matrix	brain

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