Variant report

Variant	rs2462966
Chromosome Location	chr17:38863834-38863835
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1012388	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11078950	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11650910	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11654834	0.92[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs11659024	0.95[CHD][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]
rs11869540	0.85[EUR][1000 genomes]
rs1474454	0.92[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs1526601	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16966093	0.81[EUR][1000 genomes]
rs1961204	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011870	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2272288	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429547	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2429548	0.96[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2429550	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429552	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2462957	0.96[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462960	0.96[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462961	1.00[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462965	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462967	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462969	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2469817	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469819	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469825	0.96[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55664118	0.80[EUR][1000 genomes]
rs6503545	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6503546	0.81[EUR][1000 genomes]
rs67138687	0.81[EUR][1000 genomes]
rs723728	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]
rs723729	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]
rs726849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065040	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8074758	0.96[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs874889	1.00[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs887376	1.00[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9303294	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9630729	0.81[EUR][1000 genomes]
rs9675112	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2462966	KRT24	cis	Esophagus Mucosa	GTEx
rs2462966	SMARCE1	cis	multi-tissue	Pritchard
rs2462966	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs2462966	CCL4	cis	parietal	SCAN
rs2462966	SPRY2	trans	lymphoblastoid	seeQTL
rs2462966	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs2462966	TADA2A	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38853400-38864000	Weak transcription	A549	lung
2	chr17:38853800-38864000	Weak transcription	Right Atrium	heart
3	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:38860000-38864000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:38860000-38864600	Weak transcription	Placenta	Placenta
6	chr17:38860000-38890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr17:38861600-38864200	Enhancers	Hela-S3	cervix
8	chr17:38861800-38864600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:38862200-38864200	Weak transcription	HMEC	breast
10	chr17:38862400-38864000	Weak transcription	NHEK	skin
11	chr17:38863600-38864200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:38863600-38864200	Enhancers	Spleen	Spleen
13	chr17:38863600-38864400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:38863600-38864600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:38863600-38865000	Enhancers	HUVEC	blood vessel
16	chr17:38863800-38864400	Weak transcription	Lung	lung
17	chr17:38863800-38864600	Bivalent Enhancer	HepG2	liver

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