Variant report

Variant	rs2744578
Chromosome Location	chr6:24499157-24499158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24491848..24494534-chr6:24497211..24499675,3	MCF-7	breast:
2	chr6:24493044..24496959-chr6:24499053..24507631,9	MCF-7	breast:
3	chr6:24496929..24500234-chr6:24504252..24507783,4	K562	blood:
4	chr6:24497206..24500144-chr6:24502439..24504926,2	MCF-7	breast:
5	chr6:24495638..24500234-chr6:24504925..24509115,5	K562	blood:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1126617	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12190732	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12190926	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12197859	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13193549	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1883415	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2076316	0.88[ASN][1000 genomes]
rs2076317	0.91[ASN][1000 genomes]
rs2245668	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2245674	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744567	0.82[AMR][1000 genomes]
rs2744568	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2744575	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2744577	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2744579	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2760114	0.81[EUR][1000 genomes]
rs2760115	0.81[EUR][1000 genomes]
rs2760116	0.81[EUR][1000 genomes]
rs2760117	0.81[EUR][1000 genomes]
rs2760118	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2760126	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2760129	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760131	0.80[AMR][1000 genomes]
rs2760132	0.80[AMR][1000 genomes]
rs2760140	0.82[ASN][1000 genomes]
rs2817207	0.82[ASN][1000 genomes]
rs2817211	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2817213	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817216	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2817219	0.81[EUR][1000 genomes]
rs4646830	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67103741	0.82[EUR][1000 genomes]
rs7775073	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7775307	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv965688	chr6:24498821-24503046	Strong transcription Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2744578	ALDH5A1	cis	Thyroid	GTEx
rs2744578	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL
rs2744578	ALDH5A1	cis	lung	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24495800-24517800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:24496000-24501600	Weak transcription	A549	lung
3	chr6:24496000-24513000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:24496000-24517800	Weak transcription	Spleen	Spleen
5	chr6:24496000-24534200	Weak transcription	Gastric	stomach
6	chr6:24496000-24538000	Weak transcription	Esophagus	oesophagus
7	chr6:24496200-24502200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:24496200-24502400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:24496200-24503000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:24496200-24503400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:24496200-24503600	Weak transcription	Aorta	Aorta
12	chr6:24496200-24503600	Weak transcription	Ovary	ovary
13	chr6:24496200-24503600	Weak transcription	Pancreas	Pancrea
14	chr6:24496200-24503800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:24496200-24503800	Weak transcription	Fetal Brain Female	brain
16	chr6:24496200-24504000	Weak transcription	Fetal Lung	lung
17	chr6:24496200-24505000	Weak transcription	Right Ventricle	heart
18	chr6:24496200-24506200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:24496200-24526400	Weak transcription	Right Atrium	heart
20	chr6:24496200-24527800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
24	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
25	chr6:24496400-24503400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:24496400-24503400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:24496400-24503600	Weak transcription	Fetal Kidney	kidney
28	chr6:24496400-24503800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:24496400-24517200	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:24496400-24532200	Weak transcription	Brain Germinal Matrix	brain
31	chr6:24496600-24502400	Weak transcription	Fetal Intestine Large	intestine
32	chr6:24496600-24502800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:24496600-24503200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:24496600-24503600	Weak transcription	Brain Anterior Caudate	brain
35	chr6:24496600-24503600	Weak transcription	Left Ventricle	heart
36	chr6:24496600-24504000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:24496600-24505000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:24496600-24507000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:24496600-24507400	Weak transcription	Fetal Brain Male	brain
40	chr6:24496600-24512400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:24496800-24502400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:24496800-24502400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:24496800-24503400	Weak transcription	Adipose Nuclei	Adipose
44	chr6:24496800-24503600	Weak transcription	Brain Angular Gyrus	brain
45	chr6:24496800-24503600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:24496800-24507600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:24496800-24508800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:24496800-24517600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:24496800-24522800	Weak transcription	Lung	lung
50	chr6:24496800-24532400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links