Variant report

Variant	rs7515690
Chromosome Location	chr1:170468068-170468069
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	chr1:170462398..170463942-chr1:170466713..170468804,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231407	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10919407	0.83[ASN][1000 genomes]
rs10919422	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11588124	0.82[AMR][1000 genomes]
rs11589240	0.82[AMR][1000 genomes]
rs11589376	0.82[AMR][1000 genomes]
rs11590710	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11806866	0.87[ASN][1000 genomes]
rs12071298	0.82[EUR][1000 genomes]
rs12075840	0.80[EUR][1000 genomes]
rs12729774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731618	0.80[EUR][1000 genomes]
rs12737862	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12743310	0.80[EUR][1000 genomes]
rs12747498	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12751882	0.83[ASN][1000 genomes]
rs12755330	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs1333141	0.89[JPT][hapmap]
rs1537394	0.89[JPT][hapmap]
rs16863369	0.87[ASN][1000 genomes]
rs1855220	0.87[ASN][1000 genomes]
rs34593046	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34597697	0.83[ASN][1000 genomes]
rs34621734	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35299255	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35329498	0.87[ASN][1000 genomes]
rs35392130	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35564609	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35581791	0.92[ASN][1000 genomes]
rs4488075	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61824337	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61824349	0.87[ASN][1000 genomes]
rs61824356	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61824357	0.87[ASN][1000 genomes]
rs6663850	0.82[EUR][1000 genomes]
rs6668898	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6676293	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs67243697	0.87[ASN][1000 genomes]
rs7552922	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7515690	RXRG	cis	parietal	SCAN
rs7515690	DUSP27	cis	parietal	SCAN
rs7515690	GORAB	cis	Artery Tibial	GTEx
rs7515690	SCYL3	cis	cerebellum	SCAN
rs7515690	GORAB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170464400-170471200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:170467400-170469000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:170468000-170468800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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