Variant report

Variant	rs73860475
Chromosome Location	chr3:99582702-99582703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99562459..99564499-chr3:99581056..99583363,3	MCF-7	breast:
2	chr3:99574024..99577676-chr3:99581622..99586745,5	K562	blood:
3	chr3:99575233..99577676-chr3:99581601..99584216,3	K562	blood:
4	chr3:99582314..99585905-chr3:99590964..99594499,4	MCF-7	breast:
5	chr3:99582343..99586390-chr3:99587207..99589734,4	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs57462580	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57525901	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61498368	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6783067	0.82[AFR][1000 genomes]
rs73858965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73858967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73859916	1.00[AFR][1000 genomes]
rs73859919	0.86[AFR][1000 genomes]
rs73860466	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73860468	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73860469	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73860476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7617103	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7640817	1.00[AFR][1000 genomes];1.00[AMR][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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:99565600-99589400	Weak transcription	K562	blood
7	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
8	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:99573400-99589200	Genic enhancers	HepG2	liver
10	chr3:99573600-99584800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:99574000-99584000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:99574400-99590000	Weak transcription	Liver	Liver
13	chr3:99575000-99587000	Weak transcription	Pancreas	Pancrea
14	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:99575200-99587000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:99576000-99587600	Genic enhancers	NHDF-Ad	bronchial
17	chr3:99576400-99585000	Weak transcription	A549	lung
18	chr3:99577400-99587200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:99578200-99585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:99578800-99584400	Strong transcription	Fetal Intestine Large	intestine
21	chr3:99579200-99591000	Genic enhancers	NH-A	brain
22	chr3:99579400-99583000	Weak transcription	Stomach Mucosa	stomach
23	chr3:99579400-99587000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:99579400-99591000	Weak transcription	Fetal Lung	lung
25	chr3:99579600-99584000	Weak transcription	HMEC	breast
26	chr3:99579600-99585200	Weak transcription	Small Intestine	intestine
27	chr3:99579600-99585400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:99579600-99592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:99580400-99585200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:99580400-99585200	Weak transcription	Fetal Kidney	kidney
31	chr3:99580400-99585400	Strong transcription	Fetal Muscle Leg	muscle
32	chr3:99580600-99585200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:99580600-99587000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:99580600-99587600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:99580800-99590800	Weak transcription	Lung	lung
36	chr3:99581200-99589200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:99581400-99583600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:99581400-99585400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:99581400-99585400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:99581400-99594000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:99581600-99582800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:99581600-99583000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:99581600-99583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:99581600-99585000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:99581800-99582800	Strong transcription	Adipose Nuclei	Adipose
46	chr3:99581800-99582800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
47	chr3:99581800-99582800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:99581800-99589600	Weak transcription	Gastric	stomach
49	chr3:99582000-99583200	Enhancers	GM12878-XiMat	blood
50	chr3:99582000-99583600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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