Variant report

Variant	rs10986708
Chromosome Location	chr9:101314056-101314057
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10986740	0.81[ASW][hapmap];0.84[CEU][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs12338626	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12349351	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1999498	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2779602	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs884888	0.81[ASW][hapmap];0.84[CEU][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv6633	chr9:101308371-101342811	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	esv1841097	chr9:101309058-101317401	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10986708	BARX1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101311800-101315400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:101311800-101316600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr9:101313800-101315000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr9:101313800-101315200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr9:101313800-101315600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:101314000-101314400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:101314000-101314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:101314000-101315000	Flanking Active TSS	NH-A	brain

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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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