Variant report

Variant	rs752570
Chromosome Location	chr13:52532039-52532040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52521155..52523610-chr13:52530380..52532308,2	MCF-7	breast:
2	chr13:52525579..52528317-chr13:52530342..52532434,2	K562	blood:
3	chr13:52526952..52529945-chr13:52530392..52532548,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1051332	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1801243	0.81[EUR][1000 genomes]
rs1801244	0.85[EUR][1000 genomes]
rs2031992	0.85[ASN][1000 genomes]
rs2104353	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2181891	0.81[EUR][1000 genomes]
rs2296246	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742288	0.85[EUR][1000 genomes]
rs3783241	0.94[EUR][1000 genomes]
rs3825526	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825527	0.85[EUR][1000 genomes]
rs747781	0.82[EUR][1000 genomes]
rs750290	0.81[EUR][1000 genomes]
rs754610	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999812	0.84[EUR][1000 genomes]
rs9526811	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526812	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526814	0.95[EUR][1000 genomes]
rs9535797	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563078	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568677	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568681	0.81[EUR][1000 genomes]
rs9591438	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs752570	ALG11	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
3	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:52501600-52532400	Strong transcription	HepG2	liver
6	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
10	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:52511800-52535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
14	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
15	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:52519400-52546000	Weak transcription	Spleen	Spleen
21	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr13:52523800-52532800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr13:52525200-52550200	Weak transcription	Fetal Brain Female	brain
24	chr13:52525400-52553000	Weak transcription	Ovary	ovary
25	chr13:52528000-52543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:52528200-52532600	Enhancers	Fetal Muscle Leg	muscle
27	chr13:52528200-52532800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr13:52528200-52536000	Strong transcription	Adipose Nuclei	Adipose
29	chr13:52528400-52540800	Weak transcription	Lung	lung
30	chr13:52528400-52544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:52528600-52534000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr13:52528600-52534000	Enhancers	Stomach Mucosa	stomach
33	chr13:52528600-52534200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr13:52528800-52542200	Weak transcription	Fetal Heart	heart
35	chr13:52529000-52532600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr13:52529600-52533800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:52529600-52553000	Weak transcription	Psoas Muscle	Psoas
38	chr13:52529800-52532600	Strong transcription	Aorta	Aorta
39	chr13:52529800-52537000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr13:52529800-52539200	Weak transcription	Right Ventricle	heart
41	chr13:52529800-52541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr13:52530200-52542000	Weak transcription	Brain Germinal Matrix	brain
43	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:52530400-52541600	Weak transcription	Fetal Thymus	thymus
45	chr13:52530400-52549000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr13:52530600-52534400	Weak transcription	Small Intestine	intestine
47	chr13:52530600-52550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr13:52530800-52532400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:52530800-52532400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr13:52530800-52535200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links