Variant report

Variant	rs2779600
Chromosome Location	chr9:101300786-101300787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12338626	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs12349351	0.93[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs16917019	0.82[YRI][hapmap]
rs1999498	0.92[YRI][hapmap]
rs2001993	0.88[AFR][1000 genomes]
rs2779601	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2779602	0.81[ASW][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2808522	0.81[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs2808523	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2808570	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs884887	0.84[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs884888	0.96[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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2779600	BARX1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101295800-101302400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:101298400-101304400	Weak transcription	Right Atrium	heart
3	chr9:101299400-101303000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:101300400-101302400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:101300600-101301400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:101300600-101301800	Enhancers	Fetal Brain Male	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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