Variant report

Variant	rs13300423
Chromosome Location	chr9:118113846-118113847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10982664	0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs13284742	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13286646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290701	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13293715	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13298466	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13301268	0.90[AMR][1000 genomes]
rs13301972	1.00[AFR][1000 genomes]
rs2188042	1.00[AFR][1000 genomes]
rs34302658	1.00[AFR][1000 genomes]
rs34313216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34321307	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34466382	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34471912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34568491	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34581742	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34705596	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34728021	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34748014	1.00[AFR][1000 genomes]
rs34816653	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34900397	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34928792	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34938648	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35132145	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35203429	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35259015	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35365687	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35433621	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35468444	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35483504	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35643606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35770937	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs35976675	1.00[AFR][1000 genomes]
rs36001303	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36007561	1.00[AFR][1000 genomes]
rs36078239	1.00[AFR][1000 genomes]
rs4344149	0.90[MEX][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs56199075	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57096760	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60262778	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs71505542	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs71505544	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs71505548	1.00[AFR][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	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2761552	chr9:118113846-118157488	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13300423	C9orf27	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118110800-118122400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:118112400-118115400	Weak transcription	HMEC	breast
3	chr9:118112400-118115400	Weak transcription	NHEK	skin
4	chr9:118112400-118115800	Weak transcription	NHDF-Ad	bronchial
5	chr9:118112600-118114400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:118112600-118115400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:118112800-118116000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:118112800-118121800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:118113400-118116000	Weak transcription	NHLF	lung
10	chr9:118113800-118114400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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