Variant report

Variant	rs1409371
Chromosome Location	chr20:24545732-24545733
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13039850	0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1326299	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1575873	0.85[ASN][1000 genomes]
rs1980821	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1980822	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1980823	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2018095	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4552249	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4815275	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4815278	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815279	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs6036837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6049781	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6049805	0.80[CHD][hapmap]
rs6076237	0.81[ASN][1000 genomes]
rs6076238	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083555	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6083556	0.83[ASN][1000 genomes]
rs6083558	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6083562	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6132750	0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138330	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138331	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138332	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs727409	0.80[CHD][hapmap]
rs8126241	0.90[JPT][hapmap];0.82[ASN][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	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1409371	RALGAPA2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24528800-24546400	Weak transcription	Aorta	Aorta
2	chr20:24538800-24570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:24541800-24551600	Weak transcription	Fetal Brain Male	brain
4	chr20:24542200-24552400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr20:24542400-24551800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr20:24543200-24553200	Weak transcription	Brain Substantia Nigra	brain
7	chr20:24544400-24545800	Enhancers	Brain Hippocampus Middle	brain
8	chr20:24544800-24546000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:24545400-24549200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr20:24545400-24553600	Weak transcription	Brain Anterior Caudate	brain
11	chr20:24545400-24554000	Weak transcription	Brain Angular Gyrus	brain

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