Variant report

Variant	rs1448999
Chromosome Location	chr3:159070624-159070625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11921372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13434321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375409	0.95[CEU][hapmap]
rs1449000	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1449004	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs1449013	0.95[CEU][hapmap]
rs1489922	0.86[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs1515627	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967363	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2220521	0.86[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs2621302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4086062	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679856	0.86[CEU][hapmap]
rs6441256	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6782775	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7621541	0.86[CEU][hapmap]
rs7632141	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7643870	0.91[CEU][hapmap]
rs895877	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9290040	0.86[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs9880297	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1448999	C3orf57	cis	cerebellum	SCAN
rs1448999	SCARNA7	cis	cerebellum	SCAN
rs1448999	SCHIP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159065800-159074000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:159067600-159072200	Weak transcription	Fetal Brain Male	brain

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