Variant report

Variant	rs1005789
Chromosome Location	chr5:154496941-154496942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10037186	0.88[ASN][1000 genomes]
rs10038694	0.83[AFR][1000 genomes]
rs10038971	0.82[AFR][1000 genomes]
rs10050521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10050836	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10066196	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10066219	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10066223	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10078699	0.94[ASN][1000 genomes]
rs1008795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10476812	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11167712	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13155597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319694	0.83[AFR][1000 genomes]
rs1564885	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17572520	0.90[JPT][hapmap]
rs17573136	0.93[ASN][1000 genomes]
rs35161960	0.88[ASN][1000 genomes]
rs4958779	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580136	0.83[ASN][1000 genomes]
rs6890664	0.81[AFR][1000 genomes]
rs6897414	0.94[ASN][1000 genomes]
rs7703459	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9285651	0.82[AFR][1000 genomes]
rs9324804	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9324805	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs988435	0.81[AFR][1000 genomes]
rs991314	0.82[AFR][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	nsv883059	chr5:154457905-154556230	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv462492	chr5:154489393-154523910	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv600091	chr5:154489393-154523910	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1005789	SAP30L	cis	parietal	SCAN
rs1005789	CLINT1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154496600-154498400	Weak transcription	Fetal Heart	heart
2	chr5:154496800-154497000	Active TSS	HSMMtube	muscle

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