Variant report

Variant	rs56315536
Chromosome Location	chr3:78772997-78772998
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: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11927671	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2608023	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28482804	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9837496	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9874934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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:48 , 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	chr3:78740400-78773800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
4	chr3:78752200-78773600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:78756200-78773800	Weak transcription	Fetal Kidney	kidney
7	chr3:78756800-78777800	Weak transcription	Osteobl	bone
8	chr3:78757200-78773800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:78757200-78775000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:78762800-78774000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:78763600-78773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:78764200-78777400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:78765800-78778000	Weak transcription	HMEC	breast
17	chr3:78766200-78773200	Weak transcription	Primary T cells from cord blood	blood
18	chr3:78766400-78774000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:78766400-78777400	Weak transcription	Adipose Nuclei	Adipose
20	chr3:78766400-78778000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:78766400-78778000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:78766600-78773600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:78766600-78773800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:78766600-78773800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:78766600-78773800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:78766600-78774200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:78766600-78774200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:78766600-78778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:78766600-78778000	Weak transcription	Ovary	ovary
30	chr3:78766600-78783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:78771000-78774600	Enhancers	Fetal Lung	lung
32	chr3:78771200-78774200	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:78771400-78773600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:78771400-78773800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:78771600-78774000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:78771600-78774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:78771800-78774200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:78772000-78774000	Weak transcription	A549	lung
39	chr3:78772000-78778000	Weak transcription	NHEK	skin
40	chr3:78772000-78792200	Weak transcription	HepG2	liver
41	chr3:78772200-78773200	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:78772200-78774400	Enhancers	Fetal Stomach	stomach
43	chr3:78772400-78774000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:78772600-78773000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:78772800-78773200	Enhancers	Brain Anterior Caudate	brain
46	chr3:78772800-78773400	Weak transcription	Brain Substantia Nigra	brain
47	chr3:78772800-78773800	Enhancers	Fetal Brain Male	brain
48	chr3:78772800-78776000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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