Variant report

Variant	rs12438542
Chromosome Location	chr15:78029536-78029537
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78028786..78030322-chr15:78031928..78034690,2	MCF-7	breast:
2	chr15:78021356..78025369-chr15:78027266..78032240,6	K562	blood:
3	chr15:78022100..78024937-chr15:78029389..78030939,2	MCF-7	breast:
4	chr15:78025937..78028390-chr15:78028577..78030082,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10851896	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10851897	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072664	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11072670	0.90[ASN][1000 genomes]
rs11629729	0.81[ASN][1000 genomes]
rs11630598	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11631237	0.92[ASN][1000 genomes]
rs11636173	0.90[ASN][1000 genomes]
rs11636649	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637588	0.82[ASN][1000 genomes]
rs11637968	0.90[ASN][1000 genomes]
rs12442435	0.80[ASN][1000 genomes]
rs3935682	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935683	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935684	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935685	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935831	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072803	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4073356	0.81[ASN][1000 genomes]
rs4076998	0.83[ASN][1000 genomes]
rs4468571	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886901	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886904	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58619842	0.90[ASN][1000 genomes]
rs58813188	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58831466	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60917280	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61331678	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62007780	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007781	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007784	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62009151	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67133828	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72730707	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv833061	chr15:77998374-78121905	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv570150	chr15:78004743-78038124	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv904420	chr15:78025267-78078903	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78013000-78031200	Weak transcription	Fetal Brain Female	brain
2	chr15:78014000-78031000	Weak transcription	Spleen	Spleen
3	chr15:78020800-78030200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:78026400-78029600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:78027600-78029800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:78028600-78029800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:78029400-78029800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:78029400-78030600	Flanking Active TSS	K562	blood

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