Variant report

Variant	rs1555892
Chromosome Location	chr20:24500721-24500722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13041310	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1326305	1.00[JPT][hapmap]
rs2386954	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2386956	0.89[CEU][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4283490	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036832	0.88[LWK][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6049744	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6049750	0.81[EUR][1000 genomes]
rs6049755	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6049757	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6049758	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6049759	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6049760	0.89[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6049765	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6049768	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6049771	0.88[LWK][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6049775	0.89[CEU][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6076231	0.85[CHD][hapmap];0.93[JPT][hapmap]
rs6076233	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076235	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6083539	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6114752	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6114757	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6114760	0.83[EUR][1000 genomes]
rs6132738	0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6132742	0.88[LWK][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6132743	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138309	0.85[CHD][hapmap];0.93[JPT][hapmap]
rs6138310	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6138316	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1058146	chr20:24210196-24531087	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1555892	CST9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24481600-24504200	Weak transcription	Fetal Brain Male	brain
2	chr20:24491400-24508600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:24499200-24503000	Weak transcription	Brain Hippocampus Middle	brain
4	chr20:24499400-24501400	Weak transcription	Brain Inferior Temporal Lobe	brain

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