Variant report

Variant	rs28444183
Chromosome Location	chr3:105120517-105120518
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105115312..105118076-chr3:105118161..105120646,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2033803	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59857604	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6437585	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6437586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618632	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633625	0.81[ASN][1000 genomes]
rs7640337	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650270	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7651616	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651901	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815659	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846962	0.81[ASN][1000 genomes]
rs9875972	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879039	0.81[ASN][1000 genomes]
rs9879710	0.81[ASN][1000 genomes]

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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105113400-105121200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:105113400-105121400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:105113400-105122400	Weak transcription	Primary B cells from cord blood	blood
4	chr3:105114600-105123400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:105115800-105122200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:105116800-105121400	Enhancers	Brain Substantia Nigra	brain
7	chr3:105117000-105121400	Weak transcription	Aorta	Aorta
8	chr3:105117200-105121000	Weak transcription	Pancreas	Pancrea
9	chr3:105117200-105121200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:105117200-105121200	Weak transcription	Lung	lung
11	chr3:105118400-105121000	Enhancers	NHEK	skin
12	chr3:105118400-105122200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:105118600-105120800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:105118600-105122000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:105118800-105120600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:105119000-105121200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:105119000-105122000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:105119000-105122200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:105119000-105123000	Weak transcription	Liver	Liver
20	chr3:105119000-105133600	Weak transcription	Brain Angular Gyrus	brain
21	chr3:105119200-105120600	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:105119200-105121600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:105119200-105123200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:105119400-105121200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:105119600-105120800	Enhancers	HMEC	breast
26	chr3:105119600-105121200	Flanking Active TSS	A549	lung
27	chr3:105119800-105121200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:105119800-105121400	Enhancers	HUVEC	blood vessel
29	chr3:105119800-105121400	Enhancers	Osteobl	bone
30	chr3:105119800-105121600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:105120000-105120600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr3:105120000-105121200	Weak transcription	Gastric	stomach
33	chr3:105120000-105121200	Enhancers	Stomach Mucosa	stomach
34	chr3:105120000-105121600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:105120000-105121800	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr3:105120000-105130000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:105120200-105120600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:105120200-105121000	Enhancers	Hela-S3	cervix
39	chr3:105120200-105121400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:105120200-105121400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:105120200-105121600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:105120200-105121800	Flanking Active TSS	NH-A	brain
43	chr3:105120200-105122600	ZNF genes & repeats	GM12878-XiMat	blood
44	chr3:105120400-105121000	Enhancers	NHLF	lung
45	chr3:105120400-105121200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr3:105120400-105121200	Enhancers	HSMMtube	muscle
47	chr3:105120400-105129400	Weak transcription	Brain Anterior Caudate	brain

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