Variant report

Variant	rs12208521
Chromosome Location	chr6:24465457-24465458
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10946703	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1111013	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1111014	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11758106	0.83[EUR][1000 genomes]
rs11759284	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13218564	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1810473	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34052391	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34517349	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35864956	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646828	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4712825	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62400473	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62400494	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461028	0.84[EUR][1000 genomes];0.89[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12208521	ALDH5A1	cis	Muscle Skeletal	GTEx
rs12208521	ALDH5A1	cis	lung	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
2	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:24438400-24483200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:24438800-24469200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:24447200-24470200	Weak transcription	Aorta	Aorta
7	chr6:24447400-24490400	Weak transcription	Brain Anterior Caudate	brain
8	chr6:24448200-24466200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:24448800-24488000	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:24452600-24466400	Weak transcription	Dnd41	blood
11	chr6:24453200-24471000	Strong transcription	Liver	Liver
12	chr6:24458600-24489000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:24458800-24492800	Weak transcription	Thymus	Thymus
14	chr6:24458800-24494000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:24465200-24467800	Weak transcription	Adipose Nuclei	Adipose
16	chr6:24465200-24470200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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