Variant report

Variant	rs10992474
Chromosome Location	chr9:95565979-95565980
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	chr9:95432561..95435212-chr9:95564441..95567422,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10821001	0.85[EUR][1000 genomes]
rs10821003	0.85[EUR][1000 genomes]
rs10821004	0.87[EUR][1000 genomes]
rs10821005	0.87[EUR][1000 genomes]
rs10821011	0.86[EUR][1000 genomes]
rs10821014	0.87[EUR][1000 genomes]
rs10992396	0.84[EUR][1000 genomes]
rs10992406	0.83[CEU][hapmap]
rs10992407	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10992408	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10992409	0.84[EUR][1000 genomes]
rs10992412	0.84[EUR][1000 genomes]
rs10992414	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992416	0.85[EUR][1000 genomes]
rs10992417	0.85[EUR][1000 genomes]
rs10992420	0.85[EUR][1000 genomes]
rs10992422	0.87[EUR][1000 genomes]
rs10992423	0.85[EUR][1000 genomes]
rs10992437	0.85[EUR][1000 genomes]
rs10992447	0.92[CEU][hapmap]
rs10992448	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs10992453	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs10992460	0.82[ASW][hapmap];0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10992461	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10992475	1.00[ASN][1000 genomes]
rs10992476	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11533010	0.87[EUR][1000 genomes]
rs12057034	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12236754	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs12238691	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs12684076	0.83[EUR][1000 genomes]
rs12684587	0.85[EUR][1000 genomes]
rs12685358	0.87[EUR][1000 genomes]
rs12686771	0.92[CEU][hapmap]
rs16908555	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16908560	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1853427	0.94[ASN][1000 genomes]
rs1853428	1.00[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1853429	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1974004	1.00[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2181584	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2398780	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3739605	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4141966	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56311406	0.88[EUR][1000 genomes]
rs57737182	0.88[EUR][1000 genomes]
rs58952648	0.87[EUR][1000 genomes]
rs60498616	0.87[EUR][1000 genomes]
rs7031163	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs72618187	0.91[ASN][1000 genomes]
rs753804	0.87[EUR][1000 genomes]
rs754600	0.80[EUR][1000 genomes]
rs7850075	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7855203	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7859967	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7860628	0.88[EUR][1000 genomes]
rs7863741	0.89[EUR][1000 genomes]
rs7869603	0.87[EUR][1000 genomes]
rs7871537	0.84[CEU][hapmap]
rs912261	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	esv3394460	chr9:95565031-95568629	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3435839	chr9:95565031-95568729	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10992474	OMD	cis	parietal	SCAN
rs10992474	FBP1	cis	cerebellum	SCAN
rs10992474	ANKRD19	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95558600-95569600	Weak transcription	Right Atrium	heart
2	chr9:95565800-95566000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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