Variant report

Variant	rs28809822
Chromosome Location	chr18:43690745-43690746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr18:43690411-43690757	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43683649..43685895-chr18:43688499..43690825,2	K562	blood:
2	chr18:43683437..43685755-chr18:43689293..43690887,2	MCF-7	breast:

Variant related genes	Relation type
HAUS1	TF binding region
ENSG00000152234	Chromatin interaction
ENSG00000152240	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11876373	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12604134	0.82[AFR][1000 genomes]
rs12605796	0.81[ASN][1000 genomes]
rs12606184	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12607480	0.94[ASN][1000 genomes]
rs12959543	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12963169	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1612622	0.83[ASN][1000 genomes]
rs1791406	0.81[ASN][1000 genomes]
rs1791407	0.83[ASN][1000 genomes]
rs1866322	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2467669	0.91[ASN][1000 genomes]
rs2515639	0.91[ASN][1000 genomes]
rs2578184	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2578187	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2578188	0.89[ASN][1000 genomes]
rs2578189	0.91[ASN][1000 genomes]
rs2578190	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2578193	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28372325	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28497462	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850644	0.91[ASN][1000 genomes]
rs2852362	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2852363	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28524126	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2853801	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2853802	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28715068	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28768435	0.94[ASN][1000 genomes]
rs28805990	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2886001	0.82[ASN][1000 genomes]
rs35029196	0.82[ASN][1000 genomes]
rs35122885	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35338711	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35360831	0.90[ASN][1000 genomes]
rs35657986	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3744992	0.90[ASN][1000 genomes]
rs4243278	0.87[ASN][1000 genomes]
rs4257298	0.82[ASN][1000 genomes]
rs4260155	0.92[ASN][1000 genomes]
rs4274509	0.83[ASN][1000 genomes]
rs4550555	0.82[EUR][1000 genomes]
rs474878	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4890624	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4890625	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59082804	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60986007	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71364518	0.91[ASN][1000 genomes]
rs7226736	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7229971	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7230180	0.94[ASN][1000 genomes]
rs7233665	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8083916	0.94[ASN][1000 genomes]
rs8085233	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8085773	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8088422	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8090410	0.81[ASN][1000 genomes]
rs8096643	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9946831	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9952157	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9954133	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9954534	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9958257	0.85[EUR][1000 genomes]
rs9965365	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv962965	chr18:43678008-43706302	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43685000-43691200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:43685000-43693800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr18:43685000-43694400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:43685000-43694400	Weak transcription	Esophagus	oesophagus
5	chr18:43685000-43694400	Weak transcription	Left Ventricle	heart
6	chr18:43685000-43707000	Weak transcription	Spleen	Spleen
7	chr18:43685000-43709000	Weak transcription	Pancreas	Pancrea
8	chr18:43685200-43691000	Weak transcription	Right Atrium	heart
9	chr18:43685200-43693800	Weak transcription	Aorta	Aorta
10	chr18:43685200-43696800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:43685200-43704200	Weak transcription	Psoas Muscle	Psoas
12	chr18:43685200-43704800	Weak transcription	Placenta	Placenta
13	chr18:43685200-43709000	Weak transcription	Right Ventricle	heart
14	chr18:43685200-43712600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr18:43685200-43712600	Weak transcription	Stomach Mucosa	stomach
16	chr18:43685200-43715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr18:43685200-43735600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr18:43685400-43693200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr18:43685400-43693200	Weak transcription	Fetal Lung	lung
20	chr18:43685400-43693200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr18:43685400-43693400	Weak transcription	Brain Hippocampus Middle	brain
22	chr18:43685400-43693400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr18:43685400-43693400	Weak transcription	HSMM	muscle
24	chr18:43685400-43693600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr18:43685400-43693600	Weak transcription	NH-A	brain
26	chr18:43685400-43693800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:43685400-43693800	Weak transcription	Adipose Nuclei	Adipose
28	chr18:43685400-43693800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr18:43685400-43693800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr18:43685400-43693800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr18:43685400-43693800	Weak transcription	HSMMtube	muscle
32	chr18:43685400-43694200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr18:43685400-43694200	Weak transcription	NHLF	lung
34	chr18:43685400-43694400	Weak transcription	Lung	lung
35	chr18:43685400-43694400	Weak transcription	Ovary	ovary
36	chr18:43685400-43702200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr18:43685400-43702200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr18:43685400-43703600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr18:43685400-43704200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr18:43685400-43704800	Weak transcription	Brain Substantia Nigra	brain
41	chr18:43685400-43704800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr18:43685400-43708200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr18:43685400-43709800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr18:43685400-43710600	Weak transcription	Colonic Mucosa	Colon
45	chr18:43685400-43711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr18:43685400-43711600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr18:43685400-43714800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr18:43685400-43714800	Weak transcription	NHDF-Ad	bronchial
49	chr18:43685400-43717200	Weak transcription	HepG2	liver
50	chr18:43685400-43729000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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