Variant report

Variant	rs9393559
Chromosome Location	chr6:24478433-24478434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2251547	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2744570	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744573	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744584	1.00[JPT][hapmap]
rs2744586	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2760141	0.81[EUR][1000 genomes]
rs2760144	0.81[EUR][1000 genomes]
rs2817214	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817220	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2817222	0.82[ASN][1000 genomes]
rs2817223	1.00[JPT][hapmap]
rs2817228	0.82[ASN][1000 genomes]
rs62400470	0.86[ASN][1000 genomes]
rs807516	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs807517	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9358768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	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	nsv525943	chr6:24476694-24479845	Enhancers Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9393559	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs9393559	ALDH5A1	cis	lung	GTEx
rs9393559	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 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	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
11	chr6:24471800-24481600	Strong transcription	Liver	Liver
12	chr6:24472600-24489400	Weak transcription	HepG2	liver
13	chr6:24473000-24494600	Weak transcription	Ovary	ovary

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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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