Variant report

Variant	rs73175879
Chromosome Location	chr3:119715576-119715577
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	chr3:119649143..119651386-chr3:119714883..119717444,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1054190	0.83[AMR][1000 genomes]
rs11914561	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11915898	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11916594	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11919783	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11923782	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11923854	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11927667	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1381841	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17204605	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17205095	0.95[EUR][1000 genomes]
rs17810302	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55644728	0.80[AMR][1000 genomes]
rs55658250	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55910624	0.88[AMR][1000 genomes]
rs56114552	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6765004	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs68194015	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175828	0.88[AMR][1000 genomes]
rs73175830	0.88[AMR][1000 genomes]
rs73175844	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175849	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175853	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73175858	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175860	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175862	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175863	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175864	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175870	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175873	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175880	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175886	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175888	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175891	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73175897	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73177904	0.95[EUR][1000 genomes]
rs73177905	0.95[EUR][1000 genomes]
rs73177907	0.94[EUR][1000 genomes]
rs7645180	0.97[AMR][1000 genomes];1.00[EUR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:119656600-119718400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:119665800-119716800	Weak transcription	HSMM	muscle
4	chr3:119681200-119723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:119687200-119716600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:119689000-119722600	Weak transcription	Gastric	stomach
7	chr3:119692400-119717000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:119692400-119723200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:119693600-119732200	Weak transcription	A549	lung
10	chr3:119700600-119722800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:119700800-119717000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:119701000-119720000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:119701000-119722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119701800-119717200	Weak transcription	Fetal Thymus	thymus
15	chr3:119706000-119717000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:119706200-119717000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:119707400-119716600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:119708200-119716800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:119709000-119722600	Weak transcription	Ovary	ovary
20	chr3:119709200-119723000	Weak transcription	Spleen	Spleen
21	chr3:119709400-119716800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:119709600-119717000	Weak transcription	Left Ventricle	heart
23	chr3:119710200-119716400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:119710200-119716600	Weak transcription	HMEC	breast
25	chr3:119710200-119716800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:119710200-119716800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:119710200-119719000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:119710200-119722600	Weak transcription	Stomach Mucosa	stomach
29	chr3:119710200-119730800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:119710400-119716400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:119710400-119717000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:119710400-119717200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:119710400-119722800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:119711000-119717000	Weak transcription	Dnd41	blood
35	chr3:119711400-119719200	Weak transcription	NHEK	skin
36	chr3:119711400-119729200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:119711600-119716800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:119711800-119722800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:119711800-119723200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:119712000-119716800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:119712000-119723400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:119712000-119732200	Weak transcription	HepG2	liver
43	chr3:119712200-119716800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:119712200-119717000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:119712200-119717000	Weak transcription	Fetal Intestine Large	intestine
46	chr3:119712200-119717000	Weak transcription	Fetal Stomach	stomach
47	chr3:119712200-119718000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:119712200-119718400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:119712200-119723400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:119712200-119732400	Weak transcription	NHLF	lung

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