Variant report

Variant	rs9406643
Chromosome Location	chr9:16403892-16403893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1057383	0.96[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810563	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1927619	0.89[CEU][hapmap];0.84[JPT][hapmap]
rs1999032	0.82[CEU][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4961488	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961717	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6475050	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475052	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6475053	0.82[CEU][hapmap]
rs6475054	0.93[CEU][hapmap]
rs7026798	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7035049	0.96[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7039703	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7046026	0.96[CEU][hapmap]
rs717267	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7853747	0.92[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7856438	0.82[CEU][hapmap]
rs9298764	0.89[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9406643	BNC2,LOC648570	cis	brain	BrainEAC

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16392000-16406800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16394000-16406800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:16400000-16411000	Weak transcription	NHLF	lung
4	chr9:16400600-16404000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr9:16400600-16405200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:16400600-16410200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:16400600-16413800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:16401000-16406800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:16401000-16408800	Weak transcription	A549	lung

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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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