Variant report

Variant	rs2760131
Chromosome Location	chr6:24487894-24487895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24485365..24488619-chr6:24493325..24495286,4	MCF-7	breast:
2	chr6:24487096..24491354-chr6:24491448..24495730,8	K562	blood:
3	chr6:24487824..24490266-chr6:24492770..24497111,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1126617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12190926	0.84[AMR][1000 genomes]
rs12197859	0.84[AMR][1000 genomes]
rs1883415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2076316	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2076317	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2244216	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2245668	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2245674	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2744567	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744568	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2744570	0.82[EUR][1000 genomes]
rs2744573	0.81[EUR][1000 genomes]
rs2744574	0.81[EUR][1000 genomes]
rs2744575	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2744577	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744578	0.80[AMR][1000 genomes]
rs2744579	0.86[AMR][1000 genomes]
rs2760117	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2760118	0.81[CHB][hapmap]
rs2760126	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2760129	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2760132	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760140	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760141	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760144	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2760154	0.91[ASN][1000 genomes]
rs2817207	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2817213	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2817216	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2817219	0.86[JPT][hapmap]
rs2817244	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817246	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817257	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646830	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs760903	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7775073	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7775307	0.85[AMR][1000 genomes];0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2760131	ALDH5A1	cis	multi-tissue	Pritchard
rs2760131	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL
rs2760131	ALDH5A1	cis	lung	GTEx
rs2760131	ALDH5A1	cis	Muscle Skeletal	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	chr6:24483800-24494000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:24485400-24494000	Weak transcription	Brain Angular Gyrus	brain
14	chr6:24487800-24488400	Flanking Active TSS	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links