Variant report

Variant	rs2429548
Chromosome Location	chr17:38851969-38851970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38837218..38838803-chr17:38851877..38853465,2	MCF-7	breast:
2	chr17:38841265..38844888-chr17:38849405..38853092,5	MCF-7	breast:
3	chr11:62607154..62608662-chr17:38850860..38852444,2	MCF-7	breast:
4	chr17:38471695..38474566-chr17:38851182..38854092,2	MCF-7	breast:
5	chr17:38850958..38852592-chr17:38854766..38857162,2	K562	blood:
6	chr17:38802702..38807766-chr17:38847952..38852014,4	MCF-7	breast:
7	chr17:38801632..38805923-chr17:38849683..38856183,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000131759	Chromatin interaction

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[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078950	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11650910	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11654834	0.94[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs11659024	0.81[ASW][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap]
rs11869540	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474454	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs1526601	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16966093	0.89[EUR][1000 genomes]
rs1961204	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2011870	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2272288	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2429547	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429550	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2429551	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429552	0.92[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2462957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462960	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462961	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462965	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2462966	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]
rs2462967	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2462969	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469817	0.96[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469819	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469820	0.96[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2469825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55664118	0.88[EUR][1000 genomes]
rs6503545	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs6503546	0.89[EUR][1000 genomes]
rs67138687	0.89[EUR][1000 genomes]
rs723728	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]
rs723729	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]
rs726849	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8065040	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8074758	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs874889	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]
rs887376	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]
rs9303294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9630729	0.89[EUR][1000 genomes]
rs9675112	0.89[CEU][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9894823	0.82[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][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
rs2429548	SPRY2	trans	lymphoblastoid	seeQTL
rs2429548	CCL4	cis	parietal	SCAN
rs2429548	KRT24	cis	Esophagus Mucosa	GTEx
rs2429548	TCAP	cis	parietal	SCAN
rs2429548	SMARCE1	cis	brain	seeQTL
rs2429548	TADA2A	cis	cerebellum	SCAN
rs2429548	SMARCE1	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38850000-38854000	Enhancers	Placenta	Placenta
2	chr17:38850800-38852200	Weak transcription	Fetal Lung	lung
3	chr17:38850800-38853200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:38851000-38854000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:38851600-38853000	Enhancers	Pancreas	Pancrea
6	chr17:38851800-38852200	Enhancers	HepG2	liver

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