Variant report

Variant	rs72959348
Chromosome Location	chr3:52456322-52456323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52444252..52446691-chr3:52455766..52457882,2	K562	blood:
2	chr3:52456149..52459336-chr3:52479539..52482914,3	MCF-7	breast:
3	chr3:52455484..52457043-chr3:52458911..52460495,2	K562	blood:

Variant related genes	Relation type
ENSG00000163930	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17052326	1.00[EUR][1000 genomes]
rs2577828	1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	1.00[EUR][1000 genomes]
rs2590840	1.00[EUR][1000 genomes]
rs2590841	1.00[EUR][1000 genomes]
rs4234635	1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs56866386	1.00[EUR][1000 genomes]
rs6766038	1.00[EUR][1000 genomes]
rs72947525	1.00[EUR][1000 genomes]
rs72947530	1.00[EUR][1000 genomes]
rs72947531	1.00[EUR][1000 genomes]
rs72947532	1.00[EUR][1000 genomes]
rs72947537	1.00[EUR][1000 genomes]
rs72947557	1.00[EUR][1000 genomes]
rs72965274	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52445600-52471600	Weak transcription	Gastric	stomach
2	chr3:52445800-52456800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52445800-52457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52445800-52457600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52446200-52457400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:52446200-52463000	Weak transcription	Lung	lung
7	chr3:52446200-52465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:52446200-52467800	Weak transcription	Esophagus	oesophagus
9	chr3:52446400-52470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:52446600-52457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:52446800-52457200	Weak transcription	Primary B cells from cord blood	blood
12	chr3:52446800-52457200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:52446800-52457400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:52446800-52458200	Weak transcription	HepG2	liver
15	chr3:52446800-52460000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:52446800-52462400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:52446800-52463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:52446800-52466000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:52447000-52456600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:52447000-52462800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:52447000-52464000	Weak transcription	Osteobl	bone
22	chr3:52447000-52470200	Weak transcription	Fetal Lung	lung
23	chr3:52447200-52456400	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:52447200-52456800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:52447200-52459000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:52447200-52461400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:52447200-52462400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:52447200-52462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:52447200-52462800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:52447200-52463000	Weak transcription	Left Ventricle	heart
31	chr3:52447200-52463000	Weak transcription	Right Ventricle	heart
32	chr3:52447200-52468000	Weak transcription	Colonic Mucosa	Colon
33	chr3:52447400-52462800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:52447400-52466200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:52447400-52467600	Weak transcription	NHEK	skin
36	chr3:52448200-52463000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:52448600-52456600	Weak transcription	Dnd41	blood
38	chr3:52448600-52456800	Weak transcription	Thymus	Thymus
39	chr3:52448600-52471200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:52449800-52457000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:52450000-52458000	Weak transcription	HSMM	muscle
42	chr3:52450200-52478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:52452200-52456800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:52453200-52456400	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:52453200-52457000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:52453800-52457200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr3:52454200-52456400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr3:52454200-52456800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:52454200-52457200	Strong transcription	Spleen	Spleen
50	chr3:52454200-52467600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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