Variant report

Variant	rs1526601
Chromosome Location	chr17:38835136-38835137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38830324..38832021-chr17:38833341..38835323,2	MCF-7	breast:
2	chr17:38139548..38141921-chr17:38833362..38835168,2	K562	blood:
3	chr17:38829867..38832106-chr17:38835076..38836671,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1012388	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078950	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650910	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11654834	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11659024	0.82[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs11869540	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1474454	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs16966093	0.91[EUR][1000 genomes]
rs1961204	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2011870	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272288	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2429547	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429548	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2429550	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429551	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2429552	0.92[CEU][hapmap];0.97[CHD][hapmap];0.89[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];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462960	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462961	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462965	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2462966	0.96[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462967	0.84[EUR][1000 genomes]
rs2462969	0.92[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2469817	0.96[CEU][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469819	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469820	0.96[CEU][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55664118	0.90[EUR][1000 genomes]
rs6503545	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs6503546	0.91[EUR][1000 genomes]
rs67138687	0.91[EUR][1000 genomes]
rs723728	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723729	0.92[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs726849	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8065040	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8074758	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs874889	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];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs887376	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];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9303294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9630729	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9675112	0.89[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9894823	0.82[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	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
4	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
rs1526601	SLFN11	cis	parietal	SCAN
rs1526601	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs1526601	SMARCE1	cis	multi-tissue	Pritchard
rs1526601	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs1526601	TADA2A	cis	cerebellum	SCAN
rs1526601	KRT24	cis	Esophagus Mucosa	GTEx
rs1526601	CCL4	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38835000-38835400	Enhancers	Fetal Intestine Large	intestine
2	chr17:38835000-38836000	Enhancers	Hela-S3	cervix

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