Variant report

Variant	rs2744568
Chromosome Location	chr6:24483279-24483280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24480171..24483418-chr6:24487804..24492933,6	K562	blood:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1126617	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12190732	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12190926	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12197859	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1883415	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2076316	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076317	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2244216	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2245668	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2245674	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2744567	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744575	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744577	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744578	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2744579	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2760118	0.80[ASN][1000 genomes]
rs2760126	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2760129	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2760131	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2760132	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2760140	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2760141	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2760144	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2760154	0.85[ASN][1000 genomes]
rs2817207	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817211	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817213	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2817216	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2817244	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2817246	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2817257	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4646830	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs760903	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7742282	0.85[AFR][1000 genomes]
rs7775073	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7775307	0.88[AMR][1000 genomes];0.89[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2744568	ALDH5A1	cis	Muscle Skeletal	GTEx
rs2744568	ALDH5A1	cis	Heart Left Ventricle	GTEx
rs2744568	ALDH5A1	cis	lung	GTEx

Chromatin state (count:17 , 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	chr6:24447400-24490400	Weak transcription	Brain Anterior Caudate	brain
4	chr6:24448800-24488000	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:24458600-24489000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:24458800-24492800	Weak transcription	Thymus	Thymus
7	chr6:24458800-24494000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:24470400-24483800	Weak transcription	Aorta	Aorta
9	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
10	chr6:24472600-24489400	Weak transcription	HepG2	liver
11	chr6:24473000-24494600	Weak transcription	Ovary	ovary
12	chr6:24479600-24490200	Weak transcription	Hela-S3	cervix
13	chr6:24480400-24493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:24481600-24484600	Weak transcription	Liver	Liver
15	chr6:24483200-24483800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:24483200-24483800	Enhancers	GM12878-XiMat	blood
17	chr6:24483200-24484800	Weak transcription	Brain Angular Gyrus	brain

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