Variant report

Variant	rs874004
Chromosome Location	chr9:100622118-100622119
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100616472..100617973-chr9:100620292..100623040,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10046805	0.85[AFR][1000 genomes]
rs10113907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10119795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818133	0.80[AFR][1000 genomes]
rs10818239	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11999801	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12003789	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12238579	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12341377	0.83[AFR][1000 genomes]
rs12347191	0.86[AFR][1000 genomes]
rs12348304	0.84[AFR][1000 genomes]
rs12348691	0.81[AFR][1000 genomes]
rs13300874	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301569	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1443434	0.81[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs1443435	0.81[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs1561958	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1561959	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1867277	0.83[AFR][1000 genomes]
rs1867278	0.91[YRI][hapmap]
rs1867280	0.84[AFR][1000 genomes]
rs2120263	0.88[CHB][hapmap]
rs2282192	0.88[CHB][hapmap]
rs2401639	0.81[AFR][1000 genomes]
rs2417577	0.81[CHB][hapmap]
rs3183927	0.81[CHB][hapmap]
rs3758248	0.82[AFR][1000 genomes]
rs3758249	0.81[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs3758251	0.81[CHB][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs3758253	0.82[CHB][hapmap]
rs3758254	0.81[CHB][hapmap]
rs3780420	0.81[CHB][hapmap]
rs4460498	0.86[AFR][1000 genomes]
rs4631576	0.81[CHB][hapmap]
rs4743140	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743147	0.84[CHB][hapmap]
rs6478437	0.81[AFR][1000 genomes]
rs6478450	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6586	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67449879	0.82[AMR][1000 genomes]
rs7020644	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7033315	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7043516	0.82[YRI][hapmap]
rs7357707	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851552	0.84[AFR][1000 genomes]
rs7853349	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7870125	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs894673	0.81[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs907577	0.81[CHB][hapmap];0.91[YRI][hapmap];0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs874004	FOXE1	cis	Esophagus Mucosa	GTEx
rs874004	Hs.43687	cis	multi-tissue	Pritchard
rs874004	C9orf156	cis	Thyroid	GTEx
rs874004	C9orf156	cis	Cerebellum	GTEx
rs874004	C9orf156	cis	Temporal Cortex	GTEx
rs874004	C9orf156	cis	Skin Sun Exposed Lower leg	GTEx
rs874004	C9orf156	cis	Frontal Cortex	GTEx
rs874004	C9orf156	cis	Brain Pons	GTEx
rs874004	C9orf156	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100620800-100625800	Weak transcription	Gastric	stomach
2	chr9:100621800-100622600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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