Variant report

Variant	rs723728
Chromosome Location	chr17:38876370-38876371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr17:38876276-38876395	GM12878	blood:	n/a	n/a
2	SPI1	chr17:38876078-38876374	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
KRT223P	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1012388	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078950	0.82[ASN][1000 genomes]
rs11650910	0.82[ASN][1000 genomes]
rs11654834	0.88[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs11659024	0.82[GIH][hapmap]
rs11869540	0.83[EUR][1000 genomes]
rs1474454	0.88[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1526601	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1961204	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011870	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2272288	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2429547	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429548	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2429550	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2429551	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2462957	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462960	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462961	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462965	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462966	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2462967	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2462969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469819	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469820	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469825	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6503545	0.88[CEU][hapmap]
rs723729	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];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8065040	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8074758	0.92[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs874889	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs887376	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9303294	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9675112	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs723728	KRT24	cis	Esophagus Mucosa	GTEx
rs723728	SMARCE1	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 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	chr17:38875000-38876400	Enhancers	Hela-S3	cervix
5	chr17:38875000-38879600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:38875800-38876400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:38875800-38877200	Weak transcription	A549	lung
8	chr17:38876000-38876400	Enhancers	Adipose Nuclei	Adipose

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