Variant report

Variant	rs793679
Chromosome Location	chr6:24427809-24427810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24426316..24427953-chr6:24428203..24431025,2	MCF-7	breast:
2	chr6:24423442..24426628-chr6:24427479..24429179,4	MCF-7	breast:
3	chr6:24424515..24426613-chr6:24427739..24429764,2	K562	blood:
4	chr6:24426425..24428903-chr6:24718888..24721058,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1056283	0.83[ASN][1000 genomes]
rs1277343	0.83[ASN][1000 genomes]
rs1277346	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13735	0.82[ASN][1000 genomes]
rs1742280	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1772253	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2753914	0.88[EUR][1000 genomes]
rs2753922	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793422	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2876672	0.85[ASN][1000 genomes]
rs3827640	0.82[ASN][1000 genomes]
rs6920147	0.83[ASN][1000 genomes]
rs6936856	0.82[ASN][1000 genomes]
rs7769012	0.83[ASN][1000 genomes]
rs793652	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs793654	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs793657	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs793682	0.81[ASN][1000 genomes]
rs793690	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793716	0.86[EUR][1000 genomes]
rs813226	0.85[EUR][1000 genomes]
rs9393554	0.83[ASN][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
rs793679	ALDH5A1	cis	lung	GTEx
rs793679	GPLD1	cis	Muscle Skeletal	GTEx
rs793679	ALDH5A1	cis	Muscle Skeletal	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24405400-24428200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:24407600-24428200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr6:24410000-24430800	Strong transcription	Left Ventricle	heart
5	chr6:24412200-24428200	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:24412600-24428600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:24412600-24429000	Strong transcription	Primary B cells from cord blood	blood
8	chr6:24412600-24430800	Strong transcription	Primary T cells from cord blood	blood
9	chr6:24413400-24429600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:24417400-24451800	Strong transcription	Liver	Liver
11	chr6:24420000-24428200	Strong transcription	GM12878-XiMat	blood
12	chr6:24420600-24428800	Weak transcription	Stomach Mucosa	stomach
13	chr6:24420600-24429000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:24421200-24428600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:24421200-24428600	Weak transcription	Thymus	Thymus
16	chr6:24421200-24429000	Weak transcription	NHLF	lung
17	chr6:24421200-24448800	Weak transcription	Gastric	stomach
18	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
19	chr6:24421400-24434000	Weak transcription	Fetal Brain Male	brain
20	chr6:24421600-24432000	Weak transcription	Fetal Heart	heart
21	chr6:24422400-24429400	Strong transcription	Brain Anterior Caudate	brain
22	chr6:24422400-24431400	Weak transcription	Fetal Intestine Small	intestine
23	chr6:24422400-24437400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:24422600-24428600	Weak transcription	Psoas Muscle	Psoas
25	chr6:24423400-24429000	Weak transcription	Fetal Stomach	stomach
26	chr6:24423400-24433600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:24423400-24437200	Weak transcription	Pancreas	Pancrea
28	chr6:24423400-24439400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:24423600-24428400	Weak transcription	A549	lung
30	chr6:24423600-24437200	Weak transcription	Right Ventricle	heart
31	chr6:24423800-24432000	Weak transcription	NHEK	skin
32	chr6:24424000-24432200	Weak transcription	Small Intestine	intestine
33	chr6:24424000-24456600	Weak transcription	Ovary	ovary
34	chr6:24424400-24445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr6:24425000-24429200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:24425400-24428400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:24425400-24428400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:24425400-24428400	Weak transcription	HSMM	muscle
39	chr6:24425400-24428600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:24425400-24428600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:24425400-24428600	Weak transcription	NHDF-Ad	bronchial
42	chr6:24425400-24432000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:24425400-24437200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:24425400-24439600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:24425600-24428600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:24425600-24428600	Weak transcription	HSMMtube	muscle
47	chr6:24425600-24428600	Weak transcription	NH-A	brain
48	chr6:24425600-24429200	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:24425600-24429400	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:24425800-24428000	Weak transcription	Placenta Amnion	Placenta Amnion

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