Variant report

Variant	rs1399419
Chromosome Location	chr4:91664577-91664578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10516879	0.84[CEU][hapmap]
rs1114878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11930189	0.94[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs12510662	0.85[YRI][hapmap]
rs1514733	0.81[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs17017482	0.85[AFR][1000 genomes]
rs17017486	0.81[AFR][1000 genomes]
rs17017488	0.85[YRI][hapmap]
rs17184632	0.89[YRI][hapmap]
rs1828884	0.94[CEU][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap]
rs57523538	0.87[EUR][1000 genomes]
rs58042044	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60487408	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6532239	0.89[YRI][hapmap]
rs6835028	0.89[YRI][hapmap]
rs6843193	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs6850783	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72875647	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7340943	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7340945	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7658990	0.89[YRI][hapmap]
rs7662647	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7665447	0.85[YRI][hapmap]
rs7678915	0.84[CEU][hapmap]
rs7685883	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][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	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv534470	chr4:91342219-91842807	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv428766	chr4:91618397-91768647	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1399419	IBSP	cis	parietal	SCAN
rs1399419	HERC6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:91663800-91668200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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