Variant report

Variant	rs73500109
Chromosome Location	chr13:52599703-52599704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52570761..52572532-chr13:52599540..52601096,2	K562	blood:
2	chr13:52585087..52587899-chr13:52598320..52601537,3	MCF-7	breast:
3	chr13:52592255..52594860-chr13:52597501..52600884,3	K562	blood:

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs57807149	1.00[AMR][1000 genomes]
rs58452626	1.00[AMR][1000 genomes]
rs60691453	1.00[AFR][1000 genomes]
rs60928383	1.00[AMR][1000 genomes]
rs61193099	1.00[AMR][1000 genomes]
rs73498112	1.00[AMR][1000 genomes]
rs73498144	1.00[AMR][1000 genomes]
rs73498182	1.00[AMR][1000 genomes]
rs73498183	1.00[AMR][1000 genomes]
rs73498187	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498200	1.00[AMR][1000 genomes]
rs73498201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73500103	1.00[AMR][1000 genomes]
rs73500123	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73500179	1.00[AFR][1000 genomes]
rs9591440	1.00[AMR][1000 genomes]
rs9596621	1.00[AMR][1000 genomes]
rs9989072	1.00[AMR][1000 genomes]
rs9989082	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	esv3383575	chr13:52597451-52600449	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52587000-52600000	Weak transcription	Esophagus	oesophagus
2	chr13:52587200-52600000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:52587400-52600000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:52588000-52609200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr13:52588000-52617400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:52588200-52602200	Weak transcription	Hela-S3	cervix
7	chr13:52589400-52605200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr13:52589800-52603400	Strong transcription	Placenta	Placenta
9	chr13:52589800-52605400	Strong transcription	Fetal Thymus	thymus
10	chr13:52590000-52604400	Strong transcription	Primary T cells from cord blood	blood
11	chr13:52590200-52600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:52590200-52603400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr13:52590400-52602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:52590600-52601400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr13:52590600-52604200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr13:52591000-52599800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:52591000-52604600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:52591600-52603400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr13:52591600-52603400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr13:52591600-52604000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr13:52591800-52599800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:52591800-52603600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:52591800-52603800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr13:52592000-52599800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr13:52592400-52600000	Weak transcription	Gastric	stomach
26	chr13:52592600-52601000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr13:52593400-52600800	Strong transcription	Osteobl	bone
28	chr13:52593600-52600000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr13:52593600-52600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr13:52593600-52600600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr13:52593600-52601600	Strong transcription	Dnd41	blood
32	chr13:52593600-52603000	Strong transcription	GM12878-XiMat	blood
33	chr13:52593600-52603200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr13:52593600-52603400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr13:52593800-52600000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr13:52593800-52600600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:52593800-52604200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr13:52593800-52604400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:52593800-52604600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:52594200-52600000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:52594200-52601800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:52595000-52600200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr13:52595000-52611200	Weak transcription	Psoas Muscle	Psoas
44	chr13:52595400-52600600	Strong transcription	HUVEC	blood vessel
45	chr13:52595600-52605000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:52595600-52606600	Weak transcription	Brain Angular Gyrus	brain
47	chr13:52596200-52600000	Weak transcription	NHEK	skin
48	chr13:52596600-52600000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr13:52596600-52614000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr13:52596800-52600000	Weak transcription	Lung	lung

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