Variant report

Variant	rs2408510
Chromosome Location	chr13:52514730-52514731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52508686..52511776-chr13:52512431..52515057,3	MCF-7	breast:
2	chr13:52513900..52515674-chr13:52517334..52520081,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1061472	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1801249	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924608	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1924609	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1924619	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998611	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2031992	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2282057	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282058	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3783240	0.95[ASN][1000 genomes]
rs4943044	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943045	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943046	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943048	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7139967	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7140038	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7321445	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7321909	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732774	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7328751	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs752569	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs754609	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs928169	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9316562	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs942463	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535792	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535793	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535795	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535796	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9591439	0.85[AMR][1000 genomes];0.83[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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
4	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
6	chr13:52495600-52515000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:52501600-52532400	Strong transcription	HepG2	liver
11	chr13:52502600-52514800	Weak transcription	HSMMtube	muscle
12	chr13:52502800-52518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
14	chr13:52504000-52515000	Weak transcription	K562	blood
15	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:52505600-52520800	Strong transcription	Fetal Intestine Small	intestine
18	chr13:52505600-52531800	Strong transcription	Liver	Liver
19	chr13:52505800-52527200	Strong transcription	Fetal Intestine Large	intestine
20	chr13:52506000-52517200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:52506000-52520800	Strong transcription	Adipose Nuclei	Adipose
22	chr13:52506000-52527200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr13:52506800-52524400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:52507000-52517200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr13:52507400-52517400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr13:52507400-52518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr13:52509000-52518200	Weak transcription	Esophagus	oesophagus
29	chr13:52509000-52530000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
31	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr13:52509600-52518600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr13:52509800-52514800	Weak transcription	Brain Anterior Caudate	brain
35	chr13:52509800-52515600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:52509800-52529600	Weak transcription	Small Intestine	intestine
37	chr13:52510000-52518600	Weak transcription	Spleen	Spleen
38	chr13:52510200-52514800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr13:52510200-52514800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:52510400-52515200	Weak transcription	Fetal Thymus	thymus
41	chr13:52511000-52515200	Weak transcription	Colonic Mucosa	Colon
42	chr13:52511400-52520600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr13:52511400-52520600	Strong transcription	Right Ventricle	heart
44	chr13:52511800-52535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:52512200-52514800	Weak transcription	Stomach Mucosa	stomach
46	chr13:52512400-52515600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr13:52512600-52515000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr13:52512600-52516400	Weak transcription	Gastric	stomach
49	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
50	chr13:52512800-52518000	Weak transcription	Fetal Brain Female	brain

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