Variant report

Variant	rs1883415
Chromosome Location	chr6:24491475-24491476
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:24491380-24491530	WERI-Rb-1	eye:	n/a	n/a
2	CTCF	chr6:24491324-24491552	K562	blood:	n/a	n/a
3	CTCF	chr6:24491380-24491530	HEEpiC	esophagus:	n/a	n/a
4	CTCF	chr6:24491400-24491550	HBMEC	blood vessel:	n/a	n/a
5	CTCF	chr6:24491380-24491530	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24490344..24492283-chr6:24493726..24496491,4	MCF-7	breast:
2	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
3	chr6:24489101..24491684-chr6:24493403..24495493,2	MCF-7	breast:
4	chr6:24487096..24491354-chr6:24491448..24495730,8	K562	blood:

No data

Variant related genes	Relation type
ALDH5A1	TF binding region
GPLD1	TF binding region
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1126617	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]
rs12190732	0.82[ASN][1000 genomes]
rs12190926	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12197859	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13193549	0.80[ASN][1000 genomes]
rs2076316	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076317	0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2244216	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2245668	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245674	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2744567	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744568	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744575	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744577	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744578	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2744579	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2760117	0.81[CHB][hapmap];0.88[MEX][hapmap]
rs2760118	0.82[ASW][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs2760126	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2760129	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2760131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760132	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760140	0.80[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760141	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2760144	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2760154	0.83[ASN][1000 genomes]
rs2817207	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817211	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2817213	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817214	0.81[EUR][1000 genomes]
rs2817216	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2817244	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2817246	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817257	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646830	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs760903	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7775073	1.00[ASW][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7775307	0.90[AFR][1000 genomes];0.85[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

Variant related diseases (count:1)

Disease	PMID	Source
Liver enzyme levels (alkaline phosphatase)	22001757	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1883415	ALDH5A1	cis	lymphoblastoid	seeQTL
rs1883415	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL
rs1883415	HIST1H4E	cis	cerebellum	SCAN
rs1883415	HIST1H4B	cis	cerebellum	SCAN
rs1883415	ALDH5A1	cis	cerebellum	SCAN
rs1883415	ALDH5A1	cis	multi-tissue	Pritchard
rs1883415	ALDH5A1	cis	Muscle Skeletal	GTEx
rs1883415	ALDH5A1	cis	lung	GTEx
rs1883415	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr6:24458800-24492800	Weak transcription	Thymus	Thymus
3	chr6:24458800-24494000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
5	chr6:24473000-24494600	Weak transcription	Ovary	ovary
6	chr6:24480400-24493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:24483800-24494000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:24485400-24494000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:24488000-24492000	Enhancers	Fetal Muscle Leg	muscle
10	chr6:24489000-24491600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:24489600-24492000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr6:24489800-24494600	Weak transcription	Right Atrium	heart
13	chr6:24490400-24492000	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:24490400-24492200	Enhancers	Liver	Liver
15	chr6:24490400-24494400	Weak transcription	Right Ventricle	heart
16	chr6:24490400-24494600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:24490600-24492200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:24490600-24493400	Weak transcription	Adipose Nuclei	Adipose
19	chr6:24490600-24493600	Weak transcription	HepG2	liver
20	chr6:24490600-24494400	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:24490600-24494400	Weak transcription	Hela-S3	cervix
22	chr6:24490800-24493800	Weak transcription	Brain Anterior Caudate	brain
23	chr6:24490800-24494200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:24491400-24491600	Enhancers	Fetal Thymus	thymus

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