Variant report

Variant	rs563807957
Chromosome Location	chr3:52407953-52407954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
2	chr3:52321755..52323526-chr3:52405745..52408434,2	K562	blood:
3	chr3:52406883..52409184-chr3:52415694..52419355,3	K562	blood:

Variant related genes	Relation type
ENSG00000114841	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv979834	chr3:52407592-52408592	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv590302	chr3:52407933-52428988	Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
4	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
6	chr3:52395400-52409400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
8	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
10	chr3:52399000-52409400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52399400-52409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:52400200-52409200	Weak transcription	Right Ventricle	heart
13	chr3:52401000-52409400	Weak transcription	Esophagus	oesophagus
14	chr3:52401200-52409400	Weak transcription	Colonic Mucosa	Colon
15	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:52404800-52409200	Weak transcription	Pancreas	Pancrea
17	chr3:52405000-52408400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:52405000-52409200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:52405000-52409200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:52405000-52409400	Weak transcription	Brain Angular Gyrus	brain
21	chr3:52405000-52409400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
23	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:52405600-52409200	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:52405600-52409200	Weak transcription	Lung	lung
26	chr3:52406200-52409200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:52406200-52409400	Enhancers	GM12878-XiMat	blood
28	chr3:52406400-52408000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:52406400-52408000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:52406400-52408000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:52406400-52409400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:52406400-52409400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:52406600-52408000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:52406600-52408000	Enhancers	Fetal Thymus	thymus
36	chr3:52406600-52409000	Weak transcription	Liver	Liver
37	chr3:52406600-52409200	Weak transcription	Placenta	Placenta
38	chr3:52406600-52409400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:52406600-52409400	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:52406600-52409400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:52406600-52409400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:52406800-52408000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr3:52406800-52409200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:52406800-52409200	Weak transcription	Fetal Stomach	stomach
45	chr3:52406800-52409400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:52407000-52408000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr3:52407000-52408400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:52407000-52409200	Weak transcription	Fetal Intestine Small	intestine
49	chr3:52407000-52409200	Weak transcription	Gastric	stomach
50	chr3:52407200-52409200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links