Variant report

Variant	rs1126617
Chromosome Location	chr6:24489652-24489653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24487096..24491354-chr6:24491448..24495730,8	K562	blood:
2	chr6:24487824..24490266-chr6:24492770..24497111,3	MCF-7	breast:
3	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
4	chr6:24489101..24491684-chr6:24493403..24495493,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12190732	0.82[ASN][1000 genomes]
rs12190926	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12197859	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13193549	0.80[ASN][1000 genomes]
rs1883415	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076316	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076317	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs2244216	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2245668	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2245674	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2744567	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744568	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744575	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744577	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744578	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2744579	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2744584	0.82[MEX][hapmap]
rs2760117	0.86[ASW][hapmap];0.81[CHB][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap]
rs2760118	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs2760126	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2760129	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2760131	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]
rs2760132	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760140	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760141	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2760144	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2760154	0.83[ASN][1000 genomes]
rs2817207	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817211	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2817213	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817216	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2817219	0.96[YRI][hapmap]
rs2817220	0.82[MEX][hapmap]
rs2817244	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2817246	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817257	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646830	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs760903	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7742282	0.83[AFR][1000 genomes]
rs7775073	0.81[ASW][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7775307	0.86[AMR][1000 genomes];0.90[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1126617	ALDH5A1	cis	lung	GTEx
rs1126617	ALDH5A1	cis	parietal	SCAN
rs1126617	ALDH5A1	cis	lymphoblastoid	seeQTL
rs1126617	ALDH5A1	cis	Muscle Skeletal	GTEx
rs1126617	ALDH5A1	cis	multi-tissue	Pritchard
rs1126617	ALDH5A1	cis	cerebellum	SCAN
rs1126617	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL
rs1126617	HIST1H2AJ	cis	cerebellum	SCAN

Chromatin state (count:19 , 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	chr6:24458800-24492800	Weak transcription	Thymus	Thymus
4	chr6:24458800-24494000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
6	chr6:24473000-24494600	Weak transcription	Ovary	ovary
7	chr6:24479600-24490200	Weak transcription	Hela-S3	cervix
8	chr6:24480400-24493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:24483800-24494000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:24485400-24494000	Weak transcription	Brain Angular Gyrus	brain
11	chr6:24488000-24492000	Enhancers	Fetal Muscle Leg	muscle
12	chr6:24488400-24490000	Active TSS	Liver	Liver
13	chr6:24489000-24490000	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:24489000-24490600	Enhancers	Adipose Nuclei	Adipose
15	chr6:24489000-24491600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr6:24489400-24490200	Weak transcription	Right Ventricle	heart
17	chr6:24489400-24490600	Enhancers	HepG2	liver
18	chr6:24489600-24489800	Enhancers	Right Atrium	heart
19	chr6:24489600-24492000	Enhancers	Skeletal Muscle Male	skeletal muscle

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