Variant report

Variant	rs7615949
Chromosome Location	chr3:89432683-89432684
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	chr3:89425184..89427715-chr3:89431081..89433096,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1028013	1.00[JPT][hapmap];0.88[MEX][hapmap]
rs1054750	0.82[MEX][hapmap]
rs1157607	0.82[MEX][hapmap]
rs12636710	0.82[MEX][hapmap]
rs12639506	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs13316356	0.81[CEU][hapmap]
rs1398534	0.86[CEU][hapmap]
rs1512185	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17026944	0.82[MEX][hapmap]
rs17738248	0.81[CEU][hapmap]
rs17800551	0.81[CEU][hapmap];0.93[CHD][hapmap]
rs17801001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17801031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1912966	0.82[MEX][hapmap]
rs2063590	0.86[CEU][hapmap]
rs2175670	0.86[CEU][hapmap]
rs28623022	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762717	0.82[MEX][hapmap]
rs4857497	0.81[CEU][hapmap];0.93[CHD][hapmap]
rs4857502	0.86[CEU][hapmap];0.93[CHD][hapmap]
rs57670516	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62275015	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62275016	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62275018	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62275019	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551412	1.00[JPT][hapmap]
rs6773815	0.84[CEU][hapmap]
rs6782527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6795074	0.82[MEX][hapmap]
rs6800041	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73137381	0.81[ASN][1000 genomes]
rs73137382	0.81[ASN][1000 genomes]
rs73137384	0.84[ASN][1000 genomes]
rs73137387	0.81[ASN][1000 genomes]
rs73137393	0.81[ASN][1000 genomes]
rs73137395	0.84[ASN][1000 genomes]
rs7373232	0.93[CHD][hapmap]
rs7631682	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7645408	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7650466	0.82[MEX][hapmap]
rs870898	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs870899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9310119	0.93[CHD][hapmap]
rs9821666	0.81[CEU][hapmap]
rs9829401	0.84[CEU][hapmap]
rs9832305	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9836340	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9842599	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9844971	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849029	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851954	0.80[CEU][hapmap]
rs9852380	0.85[CEU][hapmap]
rs9852594	0.93[CHD][hapmap]
rs9852722	0.86[CEU][hapmap]
rs9854073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860266	0.95[CEU][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862195	0.85[CEU][hapmap]
rs9863058	0.86[CEU][hapmap]
rs9863107	0.86[CEU][hapmap]
rs9864984	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866618	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs9868782	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875278	0.90[CEU][hapmap]
rs9883541	0.81[CEU][hapmap]
rs993186	0.81[CEU][hapmap];0.85[CHD][hapmap]
rs993187	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1001345	chr3:89368629-89444995	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1000694	chr3:89373820-89453045	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1011402	chr3:89384121-89444995	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv590928	chr3:89389507-89442369	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv516852	chr3:89402447-89442369	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1002605	chr3:89413038-89453045	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv963526	chr3:89431253-89438860	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7615949	STX19	trans	multi-tissue	Pritchard
rs7615949	EPHA3	cis	cerebellum	SCAN
rs7615949	CHMP2B	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89417800-89433600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:89428200-89435200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:89429200-89434800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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