Variant report

Variant	rs728006
Chromosome Location	chr1:223141268-223141269
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	chr1:223139734..223142413-chr1:223144467..223146092,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11487819	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378617	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2378618	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2378619	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609355	0.93[JPT][hapmap]
rs2609359	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2609366	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2609371	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789910	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2789924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789929	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789933	0.95[CEU][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2789934	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2789937	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2789945	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2789953	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2789954	0.95[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2789957	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2789958	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2789972	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34188904	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34620158	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34673329	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4317816	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4509582	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4846783	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61837491	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67420224	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946506	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs728006	ESRRG	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223129600-223143200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:223131400-223143400	Weak transcription	Fetal Lung	lung
3	chr1:223138200-223147000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:223139400-223143400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:223140000-223147800	Weak transcription	Fetal Kidney	kidney

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