Variant report

Variant	rs9963572
Chromosome Location	chr18:13313509-13313510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13313464..13315370-chr18:13333463..13336415,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12456874	0.94[CEU][hapmap]
rs12604142	0.90[JPT][hapmap]
rs12959077	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12959091	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12961452	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12969364	0.93[ASN][1000 genomes]
rs16940349	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17681406	0.86[JPT][hapmap]
rs1869496	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1869497	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2085048	0.90[EUR][1000 genomes]
rs2085050	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2187501	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2187502	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2276392	0.84[CEU][hapmap]
rs2867874	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2867875	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4570935	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4606791	0.90[EUR][1000 genomes]
rs55882226	0.89[EUR][1000 genomes]
rs59149409	0.84[ASN][1000 genomes]
rs7226901	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7227361	0.86[CEU][hapmap]
rs7230643	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7231701	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7234501	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7234675	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7236152	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7237181	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7241109	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7241410	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7241438	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7242207	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7242230	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8087505	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8092304	0.80[AMR][1000 genomes]
rs8094197	0.82[CEU][hapmap]
rs897035	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs9303783	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs930797	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs930798	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs930799	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs949259	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9948620	0.85[JPT][hapmap]
rs9952836	0.94[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs9954359	0.81[CEU][hapmap]
rs9957621	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2209	chr18:13276410-13316570	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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 miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13285000-13316200	Weak transcription	Aorta	Aorta
2	chr18:13298800-13314600	Weak transcription	Fetal Intestine Small	intestine
3	chr18:13303000-13314400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr18:13303200-13314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:13303200-13314600	Weak transcription	Colonic Mucosa	Colon
6	chr18:13303200-13316600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr18:13303200-13318600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr18:13303200-13318600	Weak transcription	Right Atrium	heart
9	chr18:13303400-13314600	Weak transcription	Fetal Lung	lung
10	chr18:13303400-13314600	Weak transcription	Fetal Stomach	stomach
11	chr18:13303600-13318600	Weak transcription	Colon Smooth Muscle	Colon
12	chr18:13304600-13315000	Weak transcription	Brain Hippocampus Middle	brain
13	chr18:13305000-13315000	Weak transcription	Brain Anterior Caudate	brain
14	chr18:13306800-13315800	Weak transcription	Adipose Nuclei	Adipose
15	chr18:13308600-13314400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr18:13308600-13314600	Weak transcription	Brain Germinal Matrix	brain
17	chr18:13309000-13315800	Weak transcription	Small Intestine	intestine
18	chr18:13309800-13315800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr18:13309800-13315800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr18:13310200-13316000	Weak transcription	Fetal Heart	heart
21	chr18:13310600-13316400	Weak transcription	Left Ventricle	heart
22	chr18:13310600-13318600	Weak transcription	Right Ventricle	heart
23	chr18:13311800-13314000	Enhancers	Thymus	Thymus
24	chr18:13311800-13315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:13312400-13313600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr18:13312400-13314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr18:13312400-13314600	Enhancers	Primary hematopoietic stem cells	blood
28	chr18:13312400-13314800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr18:13312400-13315200	Enhancers	Primary T cells from cord blood	blood
30	chr18:13312600-13313600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr18:13312600-13313800	Enhancers	Dnd41	blood
32	chr18:13312600-13314200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr18:13312600-13314200	Enhancers	Fetal Thymus	thymus
34	chr18:13312600-13315000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:13312600-13315200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr18:13312800-13313600	Flanking Active TSS	Liver	Liver
37	chr18:13312800-13314400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr18:13312800-13314600	Weak transcription	Esophagus	oesophagus
39	chr18:13313000-13313600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr18:13313000-13313800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr18:13313000-13313800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr18:13313000-13314000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr18:13313200-13313600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr18:13313200-13313600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr18:13313200-13313800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr18:13313200-13313800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr18:13313200-13313800	Enhancers	Gastric	stomach
48	chr18:13313200-13313800	Enhancers	Spleen	Spleen
49	chr18:13313400-13314000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr18:13313400-13314000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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