Variant report

Variant	rs56366004
Chromosome Location	chr3:52225565-52225566
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52224275..52227049-chr3:52256211..52258351,2	K562	blood:
2	chr3:52224034..52226671-chr3:52226883..52229368,2	K562	blood:
3	chr13:107543720..107546383-chr3:52224079..52226911,2	K562	blood:

Variant related genes	Relation type
ENSG00000242849	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11708581	1.00[AFR][1000 genomes]
rs3886875	1.00[AFR][1000 genomes]
rs55724529	1.00[AFR][1000 genomes]
rs56002041	1.00[AFR][1000 genomes]
rs73072980	0.82[AMR][1000 genomes]
rs73088802	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52217600-52231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52218800-52229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:52220200-52230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:52222200-52226200	Enhancers	Placenta	Placenta
5	chr3:52222200-52231600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:52223000-52225800	Enhancers	Duodenum Mucosa	Duodenum
7	chr3:52223000-52227000	Enhancers	Fetal Lung	lung
8	chr3:52223400-52228400	Weak transcription	Fetal Thymus	thymus
9	chr3:52223600-52226000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:52223600-52227000	Enhancers	Fetal Muscle Trunk	muscle
11	chr3:52223800-52226000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:52223800-52226200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:52223800-52227800	Enhancers	Fetal Muscle Leg	muscle
14	chr3:52224000-52226000	Enhancers	Fetal Stomach	stomach
15	chr3:52224000-52230000	Enhancers	Ovary	ovary
16	chr3:52224200-52225800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:52224200-52226000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:52224200-52226000	Enhancers	Adipose Nuclei	Adipose
19	chr3:52224200-52226000	Enhancers	NHLF	lung
20	chr3:52224200-52226200	Enhancers	NHDF-Ad	bronchial
21	chr3:52224200-52227000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:52224400-52226600	Weak transcription	Liver	Liver
23	chr3:52224600-52226000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:52224600-52226000	Enhancers	Lung	lung
25	chr3:52224600-52230800	Weak transcription	Psoas Muscle	Psoas
26	chr3:52224800-52225800	Enhancers	Spleen	Spleen
27	chr3:52224800-52226200	Enhancers	Stomach Smooth Muscle	stomach
28	chr3:52224800-52226600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:52224800-52226800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:52224800-52228400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:52224800-52229400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:52224800-52229400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:52224800-52229800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:52224800-52231400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:52225000-52226000	Enhancers	K562	blood
36	chr3:52225000-52226600	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:52225000-52226800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:52225000-52226800	Weak transcription	Brain Substantia Nigra	brain
39	chr3:52225000-52226800	Weak transcription	HSMMtube	muscle
40	chr3:52225000-52227000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:52225000-52227000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:52225000-52227000	Weak transcription	Esophagus	oesophagus
43	chr3:52225000-52228200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:52225000-52228200	Weak transcription	Fetal Intestine Small	intestine
45	chr3:52225000-52228200	Weak transcription	Small Intestine	intestine
46	chr3:52225000-52229400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:52225000-52229800	Weak transcription	Left Ventricle	heart
48	chr3:52225000-52231400	Weak transcription	NH-A	brain
49	chr3:52225200-52225600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:52225200-52225600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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