Variant report

Variant	rs11650910
Chromosome Location	chr17:38830935-38830936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1012388	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078950	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654834	0.86[EUR][1000 genomes]
rs11869540	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1474454	0.87[EUR][1000 genomes]
rs1526601	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16966093	0.89[EUR][1000 genomes]
rs1961204	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2011870	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272288	0.84[ASN][1000 genomes]
rs2429547	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2429548	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2429550	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429551	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2462957	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462960	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462961	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462965	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2462966	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2462969	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2469817	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469819	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469820	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2469825	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55664118	0.87[EUR][1000 genomes]
rs6503545	0.87[EUR][1000 genomes]
rs6503546	0.89[EUR][1000 genomes]
rs67138687	0.89[EUR][1000 genomes]
rs723728	0.82[ASN][1000 genomes]
rs723729	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs726849	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8065040	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074758	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs874889	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs887376	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9303294	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9630729	0.89[EUR][1000 genomes]
rs9675112	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11650910	SMARCE1	cis	multi-tissue	Pritchard
rs11650910	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs11650910	KRT24	cis	Esophagus Mucosa	GTEx
rs11650910	CCR7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38830800-38831000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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