Variant report

Variant	rs887376
Chromosome Location	chr17:38856662-38856663
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	chr17:38850958..38852592-chr17:38854766..38857162,2	K562	blood:
2	chr17:38796377..38799257-chr17:38854775..38858682,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1012388	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11078950	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11650910	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11654834	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11659024	0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs11869540	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1474454	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1526601	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16966093	0.84[EUR][1000 genomes]
rs1961204	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2011870	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272288	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2429547	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2429548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429550	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2429551	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2429552	0.96[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs2462957	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462960	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462961	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2462965	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462966	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]
rs2462967	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2462969	0.96[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2469817	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2469819	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2469820	1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2469825	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55664118	0.83[EUR][1000 genomes]
rs6503545	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs6503546	0.84[EUR][1000 genomes]
rs67138687	0.84[EUR][1000 genomes]
rs723728	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]
rs723729	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]
rs726849	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8065040	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8074758	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs874889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9630729	0.84[EUR][1000 genomes]
rs9675112	0.92[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9894823	0.82[CHB][hapmap];0.86[JPT][hapmap]

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
rs887376	TCAP	cis	parietal	SCAN
rs887376	TADA2A	cis	cerebellum	SCAN
rs887376	CCL4	cis	parietal	SCAN
rs887376	SMARCE1	cis	multi-tissue	Pritchard
rs887376	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs887376	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs887376	KRT24	cis	Esophagus Mucosa	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38853000-38859800	Weak transcription	Pancreas	Pancrea
2	chr17:38853200-38858400	Enhancers	Placenta Amnion	Placenta Amnion
3	chr17:38853400-38864000	Weak transcription	A549	lung
4	chr17:38853800-38859800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:38853800-38859800	Weak transcription	NHEK	skin
6	chr17:38853800-38864000	Weak transcription	Right Atrium	heart
7	chr17:38854000-38858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:38854000-38858600	Weak transcription	Hela-S3	cervix
9	chr17:38854000-38861800	Weak transcription	HMEC	breast
10	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:38856600-38856800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:38856600-38861600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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