Variant report

Variant	rs2417576
Chromosome Location	chr9:100628707-100628708
allele	C/T
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:

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10046805	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1007506	0.80[CHB][hapmap]
rs10113884	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10115216	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10117642	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10119760	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119853	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10120412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123699	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10512255	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10759975	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10759981	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818124	0.85[AMR][1000 genomes]
rs10818133	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10818175	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818213	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10818241	0.85[EUR][1000 genomes]
rs10984079	0.85[ASN][1000 genomes]
rs10984103	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984134	0.85[ASN][1000 genomes]
rs10984156	0.85[ASN][1000 genomes]
rs10984195	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs10984218	0.81[ASN][1000 genomes]
rs10984222	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10984230	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10984235	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10984253	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10984311	0.88[CHB][hapmap]
rs10984424	0.82[CHB][hapmap]
rs12004762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12006522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12341377	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12342417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347191	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12348304	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12348691	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12550872	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13286291	0.83[EUR][1000 genomes]
rs13287360	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13302470	0.82[AMR][1000 genomes]
rs1443434	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1443435	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1443436	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1561961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867277	0.85[AMR][1000 genomes]
rs1867278	0.88[CEU][hapmap]
rs1867280	0.85[AMR][1000 genomes]
rs1955143	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1955144	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955145	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2120264	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282190	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs2401639	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2417575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417086	0.81[ASN][1000 genomes]
rs28697997	0.81[ASN][1000 genomes]
rs28703314	0.82[EUR][1000 genomes]
rs3021525	0.83[ASN][1000 genomes]
rs3021526	0.85[AMR][1000 genomes]
rs3758248	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3758249	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3758250	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs3758251	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3808893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808895	0.90[CHB][hapmap]
rs3824495	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4255258	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4460498	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743139	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743142	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478437	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6478445	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6478469	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478471	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7022148	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7027221	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7031386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7032086	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7032114	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7034249	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7034336	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7034648	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7036589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037175	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037324	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7038998	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7044121	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7044799	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7048255	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72753537	0.81[ASN][1000 genomes]
rs7851552	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7851660	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7860144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866436	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7868534	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894673	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs907577	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs907581	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs925487	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9299258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9775370	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs993501	0.94[AMR][1000 genomes];0.98[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2417576	C9orf156	cis	Frontal Cortex	GTEx
rs2417576	C9orf156	cis	Temporal Cortex	GTEx
rs2417576	Hs.43687	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100627600-100629200	ZNF genes & repeats	GM12878-XiMat	blood

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