Variant report

Variant	rs1006665
Chromosome Location	chr9:84727874-84727875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10118455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10217389	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1028847	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1028848	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11139464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11139465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs12001732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12006037	0.86[EUR][1000 genomes]
rs12338553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339026	1.00[JPT][hapmap]
rs12340419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12340473	0.84[EUR][1000 genomes]
rs12341327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12341627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12342604	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12342760	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12345231	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1334759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1334760	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs1334761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs1855607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4387056	0.85[EUR][1000 genomes]
rs56362208	0.86[EUR][1000 genomes]
rs58039378	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559647	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs6559649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7023372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7033826	0.84[EUR][1000 genomes]
rs73480345	0.86[EUR][1000 genomes]
rs73648102	0.89[EUR][1000 genomes]
rs7853579	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7865884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049305	chr9:84667596-84918690	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831640	chr9:84695958-84880535	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1006665	MSL3	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:84722400-84731400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:84724800-84731800	Weak transcription	Pancreas	Pancrea
3	chr9:84727600-84730600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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