Variant report

Variant	rs2597384
Chromosome Location	chr8:20550536-20550537
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10086680	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1562785	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs17421098	0.93[EUR][1000 genomes]
rs17421308	0.88[ASN][1000 genomes]
rs2597381	0.88[ASN][1000 genomes]
rs2597383	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2597392	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2597393	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2597409	0.81[ASN][1000 genomes]
rs2616204	0.83[ASN][1000 genomes]
rs2616250	0.86[ASN][1000 genomes]
rs2616256	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4922229	0.83[ASN][1000 genomes]
rs6983045	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033511	chr8:19751299-20625091	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv530877	chr8:19873053-20593254	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1027535	chr8:20506377-20613664	Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1032450	chr8:20514995-21033577	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv539524	chr8:20514995-21033577	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2761417	chr8:20523767-20669443	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2597384	REEP4	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20540600-20557000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:20547800-20551000	Weak transcription	Brain Germinal Matrix	brain
3	chr8:20549800-20551000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr8:20550000-20551000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr8:20550000-20551200	Enhancers	Primary T cells from cord blood	blood
6	chr8:20550400-20550800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr8:20550400-20551000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr8:20550400-20551000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr8:20550400-20551200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:20550400-20551200	Weak transcription	Fetal Kidney	kidney

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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