Variant report

Variant	rs13300874
Chromosome Location	chr9:100627762-100627763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100626486..100628892-chr9:100629679..100633114,3	MCF-7	breast:
2	chr9:100626070..100628696-chr9:100630094..100631909,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10046805	0.84[AFR][1000 genomes]
rs10113907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10119795	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818239	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11999801	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12003789	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12238579	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12341377	0.81[AFR][1000 genomes]
rs12347191	0.85[AFR][1000 genomes]
rs12348304	0.82[AFR][1000 genomes]
rs13301569	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1443434	0.85[AFR][1000 genomes]
rs1443435	0.85[AFR][1000 genomes]
rs1561958	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1561959	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1867277	0.81[AFR][1000 genomes]
rs1867280	0.82[AFR][1000 genomes]
rs3758248	0.80[AFR][1000 genomes]
rs3758249	0.84[AFR][1000 genomes]
rs3758251	0.83[AFR][1000 genomes]
rs4460498	0.85[AFR][1000 genomes]
rs4743140	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478450	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6586	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67449879	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7020644	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7033315	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7357707	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851552	0.82[AFR][1000 genomes]
rs7853349	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7870125	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs874004	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894673	0.84[AFR][1000 genomes]
rs907577	0.84[AFR][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
rs13300874	C9orf156	cis	Esophagus Muscularis	GTEx
rs13300874	C9orf156	cis	Skin Sun Exposed Lower leg	GTEx
rs13300874	FOXE1	cis	Esophagus Mucosa	GTEx
rs13300874	C9orf156	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100626000-100628200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:100627600-100629200	ZNF genes & repeats	GM12878-XiMat	blood

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