Variant report

Variant	rs1926474
Chromosome Location	chr13:39558214-39558215
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	chr13:39551456..39554409-chr13:39557976..39559586,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11840611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12430086	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12857215	0.88[ASN][1000 genomes]
rs1326404	0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs1926475	0.81[ASN][1000 genomes]
rs2324160	0.81[ASN][1000 genomes]
rs3751376	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs3865000	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs6563660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6563661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6563662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6563663	0.84[ASN][1000 genomes]
rs67948555	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71439792	0.82[ASN][1000 genomes]
rs7324256	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7337269	1.00[ASN][1000 genomes]
rs7985641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995325	0.81[ASN][1000 genomes]
rs9315649	0.81[ASN][1000 genomes]
rs9566395	0.81[ASN][1000 genomes]
rs9576671	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576672	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576680	0.94[ASN][1000 genomes]
rs9576720	0.81[ASN][1000 genomes]
rs9576723	0.81[ASN][1000 genomes]
rs9594319	0.81[ASN][1000 genomes]
rs9603500	0.81[ASN][1000 genomes]
rs9888511	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1926474	LHFP	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39555400-39560600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr13:39555600-39560600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr13:39555600-39564600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr13:39555600-39564600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr13:39557200-39560600	Weak transcription	HepG2	liver
6	chr13:39558200-39558400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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