Variant report

Variant	rs667612
Chromosome Location	chr3:54649245-54649246
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1366032	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs483200	0.89[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs495532	0.82[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs496625	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs499292	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs500382	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs508907	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs551799	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs573279	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs586391	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs595040	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs595993	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs605284	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs616113	0.84[EUR][1000 genomes]
rs626074	0.92[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs661201	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs670335	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs674542	0.85[EUR][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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs667612	RRP9	cis	parietal	SCAN
rs667612	HESX1	cis	parietal	SCAN
rs667612	GNL3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54646800-54655200	Weak transcription	Brain Angular Gyrus	brain

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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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