Variant report

Variant	rs2104353
Chromosome Location	chr13:52503531-52503532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52502344..52503850-chr13:52505808..52508798,2	MCF-7	breast:
2	chr13:52025495..52027458-chr13:52501221..52503842,2	MCF-7	breast:
3	chr13:52496037..52498400-chr13:52502438..52504247,2	K562	blood:
4	chr13:52485688..52487698-chr13:52501876..52503635,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1051332	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061472	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1801243	0.80[EUR][1000 genomes]
rs1801244	0.84[EUR][1000 genomes]
rs1801249	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1924608	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1924609	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1998611	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2031992	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2181891	0.80[EUR][1000 genomes]
rs2282058	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2296246	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3742288	0.84[EUR][1000 genomes]
rs3783240	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3783241	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825526	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825527	0.84[EUR][1000 genomes]
rs4943044	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4943045	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4943046	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4943048	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7139967	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7321445	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7321909	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs732774	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7328751	0.83[ASN][1000 genomes]
rs750290	0.80[EUR][1000 genomes]
rs752569	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs752570	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754610	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7999812	0.83[EUR][1000 genomes]
rs942463	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9526811	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526812	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526814	0.81[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9535796	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs9535797	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9563078	0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568677	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568681	0.81[EUR][1000 genomes]
rs9591438	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9591439	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
rs2104353	ALG11	cis	Artery Tibial	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52481800-52506000	Weak transcription	Ovary	ovary
2	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:52487000-52507800	Weak transcription	Pancreas	Pancrea
4	chr13:52488000-52507800	Weak transcription	Brain Anterior Caudate	brain
5	chr13:52488000-52508200	Weak transcription	Brain Angular Gyrus	brain
6	chr13:52488000-52508200	Weak transcription	Brain Hippocampus Middle	brain
7	chr13:52488200-52505800	Weak transcription	Brain Germinal Matrix	brain
8	chr13:52488200-52508000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr13:52489600-52508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr13:52490000-52509400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr13:52492000-52508400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
14	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
16	chr13:52495400-52512600	Weak transcription	Colon Smooth Muscle	Colon
17	chr13:52495600-52508200	Weak transcription	Brain Substantia Nigra	brain
18	chr13:52495600-52515000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:52496200-52508200	Weak transcription	Stomach Mucosa	stomach
20	chr13:52496200-52508200	Weak transcription	Spleen	Spleen
21	chr13:52496600-52507200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:52497400-52508400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:52497600-52505800	Weak transcription	Aorta	Aorta
25	chr13:52497600-52505800	Weak transcription	Fetal Intestine Large	intestine
26	chr13:52497600-52507800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:52497600-52508000	Weak transcription	Fetal Brain Female	brain
28	chr13:52497600-52508800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:52497800-52505800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr13:52497800-52506000	Weak transcription	Adipose Nuclei	Adipose
32	chr13:52498800-52505800	Weak transcription	Fetal Muscle Leg	muscle
33	chr13:52498800-52505800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr13:52499800-52507600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr13:52500200-52508600	Weak transcription	Esophagus	oesophagus
36	chr13:52500400-52505800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:52500400-52508000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:52500400-52508600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr13:52500600-52507800	Weak transcription	Gastric	stomach
40	chr13:52500600-52507800	Weak transcription	Lung	lung
41	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr13:52501600-52504200	Strong transcription	Fetal Intestine Small	intestine
43	chr13:52501600-52532400	Strong transcription	HepG2	liver
44	chr13:52501800-52504400	Enhancers	Placenta	Placenta
45	chr13:52502000-52504200	Strong transcription	Liver	Liver
46	chr13:52502600-52514800	Weak transcription	HSMMtube	muscle
47	chr13:52502800-52503600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr13:52502800-52503800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr13:52502800-52503800	Weak transcription	Fetal Stomach	stomach
50	chr13:52502800-52506000	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links