Variant report

Variant	rs9725646
Chromosome Location	chr1:221685360-221685361
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	chr1:221684140..221685754-chr1:221914882..221917290,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10863616	0.80[ASN][1000 genomes]
rs10863618	0.88[ASN][1000 genomes]
rs10863620	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10863621	0.90[ASN][1000 genomes]
rs10863630	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863631	0.80[EUR][1000 genomes]
rs11118718	0.80[ASN][1000 genomes]
rs11118721	0.88[ASN][1000 genomes]
rs11118729	0.90[ASN][1000 genomes]
rs11118730	0.90[ASN][1000 genomes]
rs11118735	0.94[ASN][1000 genomes]
rs11118744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578091	0.88[ASN][1000 genomes]
rs12074359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1380252	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551670	0.80[ASN][1000 genomes]
rs1599087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599090	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1824360	0.90[ASN][1000 genomes]
rs1841177	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3911600	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4308983	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4336855	0.80[ASN][1000 genomes]
rs4846347	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846348	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846718	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61600912	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61817015	0.80[ASN][1000 genomes]
rs61817017	0.90[ASN][1000 genomes]
rs6696579	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6696765	0.90[ASN][1000 genomes]
rs7539333	0.80[ASN][1000 genomes]
rs9308395	0.82[ASN][1000 genomes]
rs969024	0.83[ASN][1000 genomes]
rs9726206	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9726287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727778	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729477	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9730022	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9725646	LYPLAL1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221682400-221685400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:221682600-221685400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:221683200-221686600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:221684400-221685600	Enhancers	Fetal Heart	heart
5	chr1:221684400-221686000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:221684800-221685800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:221685200-221685400	Enhancers	HUES64 Cell Line	embryonic stem cell

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