Variant report

Variant	rs56134465
Chromosome Location	chr2:172005756-172005757
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172002500..172008778-chr2:172012564..172018500,9	MCF-7	breast:
2	chr2:172004062..172006526-chr2:172009353..172011792,2	MCF-7	breast:
3	chr2:172004769..172008425-chr2:172014877..172017754,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10490606	0.81[AMR][1000 genomes]
rs13389859	0.86[EUR][1000 genomes]
rs16859167	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16859176	0.86[EUR][1000 genomes]
rs16859177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2356600	0.84[EUR][1000 genomes]
rs2356609	0.86[EUR][1000 genomes]
rs55644524	0.84[EUR][1000 genomes]
rs55885449	0.82[EUR][1000 genomes]
rs55939429	0.86[EUR][1000 genomes]
rs55991728	0.80[EUR][1000 genomes]
rs55995602	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55997598	0.84[EUR][1000 genomes]
rs56004444	0.86[EUR][1000 genomes]
rs56155163	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56155601	0.84[EUR][1000 genomes]
rs56243805	0.80[EUR][1000 genomes]
rs56267332	0.82[EUR][1000 genomes]
rs56308745	0.84[EUR][1000 genomes]
rs56382502	0.86[EUR][1000 genomes]
rs56934523	0.86[EUR][1000 genomes]
rs57733560	0.86[EUR][1000 genomes]
rs58685348	0.84[EUR][1000 genomes]
rs59841744	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60396936	0.86[EUR][1000 genomes]
rs60730419	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61105084	0.90[EUR][1000 genomes]
rs6711423	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6736045	0.86[EUR][1000 genomes]
rs6746133	0.82[EUR][1000 genomes]
rs73013435	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73013436	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73013439	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73013453	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73013465	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73017249	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73017262	0.90[EUR][1000 genomes]
rs73017268	0.90[EUR][1000 genomes]
rs73017286	0.84[EUR][1000 genomes]
rs73029214	0.86[EUR][1000 genomes]
rs73976125	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73976285	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7580756	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7591214	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9752051	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834456	chr2:171874210-172014659	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171957200-172010400	Weak transcription	HSMM	muscle
2	chr2:171973600-172011000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:171985600-172006200	Weak transcription	Esophagus	oesophagus
4	chr2:171988200-172014400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:171989400-172007000	Weak transcription	Lung	lung
6	chr2:171990000-172016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:171994000-172010400	Weak transcription	Thymus	Thymus
8	chr2:171994200-172010400	Weak transcription	Ovary	ovary
9	chr2:171995400-172012200	Weak transcription	Dnd41	blood
10	chr2:171996600-172006000	Weak transcription	Gastric	stomach
11	chr2:171996600-172015400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:171996600-172015400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:171996600-172015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:171997000-172007600	Weak transcription	Placenta	Placenta
15	chr2:171997000-172010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:171998200-172007200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:171998200-172010400	Weak transcription	Psoas Muscle	Psoas
18	chr2:171998400-172014800	Weak transcription	Brain Anterior Caudate	brain
19	chr2:171999000-172014800	Weak transcription	Osteobl	bone
20	chr2:171999200-172014000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:171999600-172012200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:171999600-172013800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:171999800-172006000	Weak transcription	Small Intestine	intestine
24	chr2:172000000-172010400	Weak transcription	Spleen	Spleen
25	chr2:172000200-172014600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:172001000-172010800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:172001600-172010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:172001800-172006200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:172002000-172007600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:172002600-172006400	Enhancers	HepG2	liver
31	chr2:172003000-172006000	Weak transcription	Pancreas	Pancrea
32	chr2:172003000-172006200	Weak transcription	Left Ventricle	heart
33	chr2:172003000-172012200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:172003200-172007600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:172003200-172015400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr2:172003400-172008800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:172003400-172010400	Weak transcription	Fetal Thymus	thymus
38	chr2:172003400-172012200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:172003600-172006000	Weak transcription	Fetal Intestine Large	intestine
40	chr2:172003600-172008400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:172003600-172010800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:172003600-172014600	Weak transcription	HMEC	breast
43	chr2:172003800-172010400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:172003800-172012400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:172003800-172014600	Weak transcription	NH-A	brain
46	chr2:172004000-172005800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr2:172004000-172006000	Weak transcription	Stomach Mucosa	stomach
48	chr2:172004000-172006800	Weak transcription	A549	lung
49	chr2:172004000-172010400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:172004000-172012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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