Variant report

Variant	rs723729
Chromosome Location	chr17:38876409-38876410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012388	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078950	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11650910	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11654834	0.88[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs11659024	0.90[CHD][hapmap]
rs1474454	0.88[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1526601	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1961204	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011870	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2272288	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2429547	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429548	0.92[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2429550	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2429551	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2462957	0.92[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462960	0.92[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462961	0.96[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462965	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462966	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2462967	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2462969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462970	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2469817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469819	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469820	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469825	0.92[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6503545	0.88[CEU][hapmap]
rs723728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8065040	0.82[ASN][1000 genomes]
rs8074758	0.92[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs874889	0.96[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs887376	0.96[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9303294	0.92[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9675112	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv908226	chr17:38876409-39003217	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs723729	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs723729	CCL4	cis	parietal	SCAN
rs723729	KRT24	cis	Esophagus Mucosa	GTEx
rs723729	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs723729	FLJ43826	cis	parietal	SCAN
rs723729	SMARCE1	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38860000-38890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:38874400-38878600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr17:38874800-38876600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr17:38875000-38879600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:38875800-38877200	Weak transcription	A549	lung
6	chr17:38876400-38877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:38876400-38878600	Weak transcription	Hela-S3	cervix

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