Variant report

Variant	rs1370465
Chromosome Location	chr11:16394068-16394069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1000565	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1039508	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11603071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes]
rs11608205	0.83[AFR][1000 genomes]
rs12292172	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12790582	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes]
rs1503452	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs1847315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs35503644	0.80[EUR][1000 genomes]
rs35944766	0.91[AFR][1000 genomes]
rs66705712	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66906527	0.80[EUR][1000 genomes]
rs67280587	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7930085	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7932807	0.96[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs7945007	0.86[CHB][hapmap]
rs7945099	0.96[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs7946119	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][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	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv832075	chr11:16391700-16490934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1370465	C11orf58	cis	cerebellum	SCAN
rs1370465	NUCB2	cis	lymphoblastoid	seeQTL
rs1370465	NAV2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16388200-16397000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:16388200-16414200	Weak transcription	Fetal Intestine Small	intestine
3	chr11:16389200-16397800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:16394000-16395200	Enhancers	K562	blood

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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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