Variant report

Variant	rs10459096
Chromosome Location	chr12:7586595-7586596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10444429	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10772247	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10772330	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10772331	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10772338	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10845124	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845159	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs10845176	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10845177	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10845178	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11053688	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11053769	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11053788	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12321231	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072798	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58195891	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133310	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350216	chr12:7432676-7604018	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10459096	NANOGNB	cis	cerebellum	SCAN
rs10459096	NDUFA9	cis	cerebellum	SCAN
rs10459096	PLEKHG6	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:7527600-7591200	Weak transcription	Placenta	Placenta
2	chr12:7582600-7592200	Weak transcription	Adipose Nuclei	Adipose
3	chr12:7583800-7587200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:7584200-7587000	Enhancers	NHDF-Ad	bronchial
5	chr12:7585000-7586600	Enhancers	HMEC	breast
6	chr12:7585000-7586600	Enhancers	NHEK	skin
7	chr12:7586000-7591400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:7586400-7588200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:7586400-7589000	Enhancers	HUVEC	blood vessel
10	chr12:7586400-7590600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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