Variant report

Variant	rs726863
Chromosome Location	chr1:152400361-152400362
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	chr1:152398888..152401271-chr1:152403160..152405012,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10788835	0.81[JPT][hapmap]
rs10888486	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204982	0.81[JPT][hapmap]
rs11204985	0.81[JPT][hapmap]
rs11204986	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs11204987	0.81[JPT][hapmap]
rs11205001	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11301808	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11583558	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11590822	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11803108	0.81[JPT][hapmap]
rs12024486	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12029431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12048587	0.85[ASN][1000 genomes]
rs12049036	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12403031	0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs12408401	0.84[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12568784	0.81[JPT][hapmap]
rs13374172	0.82[ASW][hapmap]
rs1858485	0.81[JPT][hapmap]
rs1923491	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs1923493	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1923505	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1923509	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2065954	0.81[JPT][hapmap]
rs2146117	0.83[CEU][hapmap]
rs2146119	0.81[JPT][hapmap]
rs2146121	0.84[ASN][1000 genomes]
rs2282303	0.80[JPT][hapmap]
rs3120665	0.81[JPT][hapmap]
rs3753443	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753444	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753446	0.85[ASN][1000 genomes]
rs3829868	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4285700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4378206	0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs45541239	0.81[AMR][1000 genomes]
rs4845766	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs6587668	0.81[AMR][1000 genomes]
rs6679449	0.81[JPT][hapmap]
rs6679899	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693160	0.81[AMR][1000 genomes]
rs6696556	0.83[CEU][hapmap]
rs726865	0.90[ASN][1000 genomes]
rs7515448	0.81[JPT][hapmap];0.85[MEX][hapmap]
rs7521839	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7555924	0.82[ASN][1000 genomes]
rs9633410	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs726863	S100A6	cis	cerebellum	SCAN
rs726863	S100A7A	cis	parietal	SCAN
rs726863	S100A7	cis	cerebellum	SCAN
rs726863	GABPB2	cis	cerebellum	SCAN
rs726863	IVL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152399600-152400600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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