Variant report

Variant	rs7742453
Chromosome Location	chr6:24484259-24484260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24483355..24485478-chr6:24495554..24497195,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11962469	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16889387	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16889391	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35206652	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761793	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56761969	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56763150	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57186149	0.89[AFR][1000 genomes]
rs58479700	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59061545	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60251819	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60816578	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61157495	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61280878	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6456617	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901703	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6902445	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6910460	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6911965	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916802	0.84[EUR][1000 genomes]
rs6928435	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7738679	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7742653	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7742675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7748068	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760684	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760930	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765441	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7765515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766241	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7766290	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295625	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461023	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9467176	0.84[EUR][1000 genomes]
rs9467182	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9467190	0.86[EUR][1000 genomes];0.85[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	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv883480	chr6:24481299-24507519	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7742453	ALDH5A1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:24447400-24490400	Weak transcription	Brain Anterior Caudate	brain
3	chr6:24448800-24488000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:24458600-24489000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:24458800-24492800	Weak transcription	Thymus	Thymus
6	chr6:24458800-24494000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
8	chr6:24472600-24489400	Weak transcription	HepG2	liver
9	chr6:24473000-24494600	Weak transcription	Ovary	ovary
10	chr6:24479600-24490200	Weak transcription	Hela-S3	cervix
11	chr6:24480400-24493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:24481600-24484600	Weak transcription	Liver	Liver
13	chr6:24483200-24484800	Weak transcription	Brain Angular Gyrus	brain
14	chr6:24483800-24494000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links