Variant report

Variant	rs13290457
Chromosome Location	chr9:118067966-118067967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11787534	0.86[CEU][hapmap]
rs11789911	1.00[MEX][hapmap]
rs34693706	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71505536	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3431886	chr9:118064781-118068179	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
3	nsv527294	chr9:118067966-118068722	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13290457	C9orf29	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118060000-118073200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:118067200-118068400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:118067400-118068200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:118067400-118068200	Flanking Active TSS	NHEK	skin
5	chr9:118067400-118068400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:118067400-118068400	Enhancers	HMEC	breast
7	chr9:118067400-118068600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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