Variant report

Variant	rs1407688
Chromosome Location	chr13:53780924-53780925
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	chr13:53780514..53781229-chr13:53805968..53806821,3	MCF-7	breast:
2	chr13:53780331..53781277-chr13:53806298..53806833,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12860317	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs1322948	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1322953	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1322954	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1322960	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1343603	0.82[EUR][1000 genomes]
rs1407689	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1885767	0.88[EUR][1000 genomes]
rs1909650	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1923770	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923772	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1951724	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1951725	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2004422	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2038647	0.81[EUR][1000 genomes]
rs2038648	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2759674	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2759713	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2759714	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2806937	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2806940	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2806947	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2806965	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2806968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806985	0.81[EUR][1000 genomes]
rs2806994	0.85[EUR][1000 genomes]
rs4886312	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5008125	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050969	chr13:53665927-54064861	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1834091	chr13:53774627-53784083	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a
3	esv1838050	chr13:53774627-53784083	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a
4	esv1835986	chr13:53774627-53786026	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a
5	esv1840677	chr13:53774627-53791895	Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53776200-53781800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:53778600-53781800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:53780800-53782200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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