Variant report

Variant	rs58080002
Chromosome Location	chr3:52125551-52125552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52125379..52127206-chr3:52129212..52131778,2	MCF-7	breast:
2	chr3:52111491..52114530-chr3:52124287..52129242,4	K562	blood:
3	chr3:52095912..52098452-chr3:52124291..52126247,2	K562	blood:
4	chr3:52124027..52125653-chr3:52126066..52128090,2	MCF-7	breast:
5	chr3:52125293..52126965-chr3:52127079..52129013,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256097	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11713464	1.00[ASN][1000 genomes]
rs11716756	1.00[ASN][1000 genomes]
rs17259762	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743840	1.00[ASN][1000 genomes]
rs58879205	1.00[ASN][1000 genomes]
rs67767125	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
6	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:52110000-52126000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52110000-52126000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52110000-52127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52110000-52127200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52110000-52127400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:52111200-52127000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:52115800-52133000	Weak transcription	Gastric	stomach
11	chr3:52119200-52126800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:52119200-52127200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:52119200-52128400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:52119200-52128600	Enhancers	Fetal Muscle Trunk	muscle
15	chr3:52119600-52129000	Enhancers	Fetal Muscle Leg	muscle
16	chr3:52120600-52126200	Enhancers	Adipose Nuclei	Adipose
17	chr3:52120600-52126600	Enhancers	Left Ventricle	heart
18	chr3:52120600-52128800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:52120600-52128800	Enhancers	Placenta	Placenta
20	chr3:52120600-52129200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:52120800-52125800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:52120800-52125800	Enhancers	K562	blood
23	chr3:52120800-52127400	Enhancers	Right Atrium	heart
24	chr3:52121000-52126200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:52121000-52128400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:52121000-52128400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:52121200-52128400	Enhancers	NHDF-Ad	bronchial
28	chr3:52121400-52129000	Weak transcription	Primary T cells from cord blood	blood
29	chr3:52121600-52126200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:52121800-52126200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:52122000-52126200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:52122000-52140000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:52122200-52125600	Genic enhancers	Fetal Intestine Small	intestine
34	chr3:52122200-52126000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:52122200-52126200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52122200-52126400	Enhancers	Fetal Lung	lung
37	chr3:52122200-52128200	Enhancers	Brain Hippocampus Middle	brain
38	chr3:52122400-52126000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:52122400-52126600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:52122400-52126600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:52122400-52130400	Enhancers	Fetal Heart	heart
42	chr3:52122600-52125800	Weak transcription	Esophagus	oesophagus
43	chr3:52122600-52127000	Enhancers	Brain Cingulate Gyrus	brain
44	chr3:52122600-52131000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:52122800-52129200	Weak transcription	GM12878-XiMat	blood
46	chr3:52122800-52142200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:52123000-52125600	Enhancers	Fetal Brain Male	brain
48	chr3:52123000-52126200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:52123000-52126600	Enhancers	Brain Angular Gyrus	brain
50	chr3:52123400-52125800	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links