Variant report

Variant	rs2817246
Chromosome Location	chr6:24472336-24472337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1126617	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1883415	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076316	0.84[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2076317	0.84[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap]
rs2244216	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2744567	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744568	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744575	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2744577	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2760117	0.86[JPT][hapmap];0.81[MEX][hapmap]
rs2760118	0.89[CHD][hapmap]
rs2760131	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760132	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760141	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2760154	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817207	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817211	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817213	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2817219	0.86[JPT][hapmap]
rs2817244	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646830	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs760903	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7775073	0.89[CHD][hapmap]
rs9358768	0.81[EUR][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	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2817246	ALDH5A1	cis	lymphoblastoid	seeQTL
rs2817246	ALDH5A1	cis	cerebellum	SCAN
rs2817246	ALDH5A1	cis	parietal	SCAN
rs2817246	ALDH5A1	cis	lung	GTEx
rs2817246	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL
rs2817246	HIST1H2AJ	cis	cerebellum	SCAN
rs2817246	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs2817246	ALDH5A1	cis	Muscle Skeletal	GTEx

Chromatin state (count:18 , 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	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:24438400-24483200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:24447400-24490400	Weak transcription	Brain Anterior Caudate	brain
5	chr6:24448800-24488000	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:24458600-24489000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:24458800-24492800	Weak transcription	Thymus	Thymus
8	chr6:24458800-24494000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:24470400-24483800	Weak transcription	Aorta	Aorta
10	chr6:24470600-24472400	Weak transcription	Osteobl	bone
11	chr6:24470600-24477000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
13	chr6:24471800-24481600	Strong transcription	Liver	Liver
14	chr6:24472000-24472400	Enhancers	Hela-S3	cervix
15	chr6:24472200-24472600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:24472200-24472800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:24472200-24473000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr6:24472200-24473000	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links