Variant report

Variant	rs1264764
Chromosome Location	chr10:116947148-116947149
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	chr10:116940963..116942966-chr10:116944377..116947212,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11498596	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12253499	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1264750	0.87[EUR][1000 genomes]
rs1264755	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1264770	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs1264773	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap]
rs1264778	0.84[EUR][1000 genomes]
rs1264781	0.90[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap]
rs1264797	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1264798	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1264801	0.86[EUR][1000 genomes]
rs1264803	0.86[EUR][1000 genomes]
rs1269601	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1565833	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs1615076	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1889610	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2165988	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2201363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2256563	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2485971	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs2587461	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs615905	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]
rs650060	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]
rs9630104	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9630105	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]

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	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv831998	chr10:116847998-116969618	Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv869279	chr10:116884639-117032437	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv868940	chr10:116933802-117032437	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1264764	EIF3A	cis	parietal	SCAN
rs1264764	PRLHR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116926600-116951400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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