Variant report

Variant	rs3773232
Chromosome Location	chr3:78774255-78774256
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	chr3:78772880..78774546-chr3:78776083..78778103,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11127631	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11127632	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083361	0.83[EUR][1000 genomes]
rs13093540	0.85[EUR][1000 genomes]
rs1350366	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17016456	1.00[CEU][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs1865862	0.81[MEX][hapmap]
rs2043661	1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs3773233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773241	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773244	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807536	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	chr3:78766600-78778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:78766600-78778000	Weak transcription	Ovary	ovary
16	chr3:78766600-78783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:78771000-78774600	Enhancers	Fetal Lung	lung
18	chr3:78772000-78778000	Weak transcription	NHEK	skin
19	chr3:78772000-78792200	Weak transcription	HepG2	liver
20	chr3:78772200-78774400	Enhancers	Fetal Stomach	stomach
21	chr3:78772800-78776000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:78773000-78775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:78773200-78775000	Weak transcription	Brain Anterior Caudate	brain
24	chr3:78773400-78776200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:78773600-78774400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:78773600-78774400	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:78773600-78776000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:78773600-78776200	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:78773800-78774400	Enhancers	Brain Germinal Matrix	brain
30	chr3:78773800-78774600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:78773800-78774600	Enhancers	Primary T cells from cord blood	blood
32	chr3:78773800-78774600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:78773800-78774600	Enhancers	Fetal Kidney	kidney
34	chr3:78773800-78775000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:78773800-78775000	Enhancers	Rectal Smooth Muscle	rectum
36	chr3:78773800-78776200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:78773800-78776200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr3:78773800-78777600	Weak transcription	Fetal Brain Male	brain
39	chr3:78774000-78774400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:78774000-78774400	Active TSS	Brain Substantia Nigra	brain
41	chr3:78774000-78774600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr3:78774000-78775400	Enhancers	A549	lung
43	chr3:78774000-78775800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:78774000-78776200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr3:78774200-78774400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr3:78774200-78774400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:78774200-78774400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:78774200-78775000	Enhancers	Colon Smooth Muscle	Colon
49	chr3:78774200-78775800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:78774200-78776000	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links