Variant report

Variant	rs73109774
Chromosome Location	chr3:78774189-78774190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78772880..78774546-chr3:78776083..78778103,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10049014	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10049102	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10428105	0.81[ASN][1000 genomes]
rs11917512	0.82[ASN][1000 genomes]
rs11919682	0.87[ASN][1000 genomes]
rs11925970	0.81[ASN][1000 genomes]
rs11927666	0.81[ASN][1000 genomes]
rs11928868	0.82[ASN][1000 genomes]
rs12106862	0.81[ASN][1000 genomes]
rs1395784	0.81[ASN][1000 genomes]
rs1457659	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17016453	0.81[ASN][1000 genomes]
rs17016466	0.81[ASN][1000 genomes]
rs17303276	0.81[ASN][1000 genomes]
rs17375110	0.81[ASN][1000 genomes]
rs17375496	0.81[ASN][1000 genomes]
rs17375739	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1865860	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1865861	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1865863	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1961636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28494803	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732663	0.81[ASN][1000 genomes]
rs3773227	0.81[ASN][1000 genomes]
rs3773231	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773234	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773239	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773240	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773245	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821602	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821603	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4263256	0.81[ASN][1000 genomes]
rs56077922	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58423115	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61053911	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67137735	0.81[ASN][1000 genomes]
rs67347336	0.81[ASN][1000 genomes]
rs67498832	0.81[ASN][1000 genomes]
rs6769933	0.81[ASN][1000 genomes]
rs6787349	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788434	0.81[ASN][1000 genomes]
rs6788511	0.81[ASN][1000 genomes]
rs6806079	0.81[ASN][1000 genomes]
rs73109717	0.81[ASN][1000 genomes]
rs73109772	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73850750	0.81[ASN][1000 genomes]
rs7622194	0.81[ASN][1000 genomes]
rs7624482	0.81[ASN][1000 genomes]
rs767182	0.81[ASN][1000 genomes]
rs9309814	0.81[ASN][1000 genomes]
rs9808950	0.82[ASN][1000 genomes]
rs9819398	0.91[ASN][1000 genomes]
rs9840033	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9861603	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866912	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9880072	0.81[ASN][1000 genomes]
rs9880316	0.81[ASN][1000 genomes]
rs9882811	0.81[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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv1842222	chr3:78744206-78778901	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78733800-78778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
3	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:78756800-78777800	Weak transcription	Osteobl	bone
5	chr3:78757200-78775000	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:78764200-78777400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:78765800-78778000	Weak transcription	HMEC	breast
11	chr3:78766400-78777400	Weak transcription	Adipose Nuclei	Adipose
12	chr3:78766400-78778000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:78766400-78778000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:78766600-78774200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:78766600-78774200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:78766600-78778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:78766600-78778000	Weak transcription	Ovary	ovary
18	chr3:78766600-78783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:78771000-78774600	Enhancers	Fetal Lung	lung
20	chr3:78771200-78774200	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:78771600-78774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:78771800-78774200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:78772000-78778000	Weak transcription	NHEK	skin
24	chr3:78772000-78792200	Weak transcription	HepG2	liver
25	chr3:78772200-78774400	Enhancers	Fetal Stomach	stomach
26	chr3:78772800-78776000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:78773000-78775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:78773200-78775000	Weak transcription	Brain Anterior Caudate	brain
29	chr3:78773400-78776200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:78773600-78774400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:78773600-78774400	Enhancers	Stomach Smooth Muscle	stomach
32	chr3:78773600-78776000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:78773600-78776200	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:78773800-78774200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr3:78773800-78774400	Enhancers	Brain Germinal Matrix	brain
36	chr3:78773800-78774600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:78773800-78774600	Enhancers	Primary T cells from cord blood	blood
38	chr3:78773800-78774600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:78773800-78774600	Enhancers	Fetal Kidney	kidney
40	chr3:78773800-78775000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:78773800-78775000	Enhancers	Rectal Smooth Muscle	rectum
42	chr3:78773800-78776200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr3:78773800-78776200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:78773800-78777600	Weak transcription	Fetal Brain Male	brain
45	chr3:78774000-78774400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr3:78774000-78774400	Active TSS	Brain Substantia Nigra	brain
47	chr3:78774000-78774600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr3:78774000-78775400	Enhancers	A549	lung
49	chr3:78774000-78775800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:78774000-78776200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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