Variant report

Variant	rs6478450
Chromosome Location	chr9:100631986-100631987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10113907	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10119795	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10818239	0.84[EUR][1000 genomes]
rs11999801	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12003789	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12238579	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13300874	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13301569	0.83[EUR][1000 genomes]
rs1561958	0.85[EUR][1000 genomes]
rs1561959	0.84[EUR][1000 genomes]
rs4743140	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6586	0.86[EUR][1000 genomes]
rs67449879	0.83[EUR][1000 genomes]
rs7020644	0.86[EUR][1000 genomes]
rs7033315	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7357707	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7853349	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7870125	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs874004	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6478450	C9orf156	cis	Esophagus Muscularis	GTEx
rs6478450	C9orf156	cis	Thyroid	GTEx
rs6478450	C9orf156	cis	Skin Sun Exposed Lower leg	GTEx
rs6478450	FOXE1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100631600-100632000	Flanking Active TSS	Hela-S3	cervix
2	chr9:100631800-100635800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:100631800-100636000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:100631800-100636200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:100631800-100639400	Weak transcription	H9 Cell Line	embryonic stem cell

Quick Search:

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

what's new

Quick links