Variant report

Variant	rs793690
Chromosome Location	chr6:24432009-24432010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24430844..24432891-chr6:24519902..24523248,3	MCF-7	breast:
2	chr6:24413201..24415525-chr6:24429958..24432815,2	K562	blood:
3	chr6:24431387..24432156-chr6:24520936..24521780,2	K562	blood:
4	chr6:24431522..24434175-chr6:24447084..24450027,2	MCF-7	breast:
5	chr6:24430350..24432062-chr6:24520550..24521835,7	MCF-7	breast:
6	chr6:24413201..24415774-chr6:24431315..24432878,2	K562	blood:

Variant related genes	Relation type
ENSG00000112294	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1277343	0.80[ASN][1000 genomes]
rs1277346	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1742280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772253	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2753914	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2753922	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2793422	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2876672	0.82[ASN][1000 genomes]
rs793652	0.87[ASN][1000 genomes]
rs793654	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs793657	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs793679	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793680	0.81[ASN][1000 genomes]
rs793682	0.84[ASN][1000 genomes]
rs793684	0.82[ASN][1000 genomes]
rs793686	0.80[ASN][1000 genomes]
rs793687	0.80[ASN][1000 genomes]
rs793716	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs813226	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs793690	GPLD1	cis	Muscle Skeletal	GTEx
rs793690	ALDH5A1	cis	Muscle Skeletal	GTEx
rs793690	ALDH5A1	cis	lung	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24417400-24451800	Strong transcription	Liver	Liver
3	chr6:24421200-24448800	Weak transcription	Gastric	stomach
4	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
5	chr6:24421400-24434000	Weak transcription	Fetal Brain Male	brain
6	chr6:24422400-24437400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:24423400-24433600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:24423400-24437200	Weak transcription	Pancreas	Pancrea
9	chr6:24423400-24439400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:24423600-24437200	Weak transcription	Right Ventricle	heart
11	chr6:24424000-24432200	Weak transcription	Small Intestine	intestine
12	chr6:24424000-24456600	Weak transcription	Ovary	ovary
13	chr6:24424400-24445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:24425400-24437200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:24425400-24439600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:24426000-24438800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:24426200-24446000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:24426400-24432400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:24426400-24441600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:24426400-24446000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:24426600-24438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:24427200-24433800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:24427400-24435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:24427600-24432400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:24427600-24433800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:24427600-24436600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:24427600-24437600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:24427600-24439200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:24427600-24439400	Weak transcription	Fetal Thymus	thymus
30	chr6:24427600-24440000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:24427600-24440000	Weak transcription	Dnd41	blood
32	chr6:24427600-24441800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:24427600-24445600	Weak transcription	Fetal Brain Female	brain
34	chr6:24427600-24456800	Weak transcription	Lung	lung
35	chr6:24427800-24435800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
37	chr6:24428200-24432600	Weak transcription	GM12878-XiMat	blood
38	chr6:24428200-24438000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:24428200-24449400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:24428800-24445000	Weak transcription	Psoas Muscle	Psoas
41	chr6:24429000-24447800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
43	chr6:24429200-24455600	Weak transcription	Brain Angular Gyrus	brain
44	chr6:24429400-24437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:24429400-24438600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr6:24429400-24445000	Weak transcription	Brain Anterior Caudate	brain
47	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:24429600-24432800	Weak transcription	Adipose Nuclei	Adipose
49	chr6:24429600-24433600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:24429600-24436600	Weak transcription	Fetal Muscle Leg	muscle

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