Variant report

Variant	rs153144
Chromosome Location	chr5:52300246-52300247
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	chr5:52299602..52301517-chr5:52301947..52304132,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3212697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35237	1.00[AFR][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	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52300400	Weak transcription	Gastric	stomach
2	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
3	chr5:52286200-52313600	Weak transcription	Lung	lung
4	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
5	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52292400-52301000	Weak transcription	Spleen	Spleen
7	chr5:52292400-52303200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:52293600-52304000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:52293800-52313400	Weak transcription	Fetal Intestine Small	intestine
10	chr5:52294200-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:52294600-52302400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:52294600-52302600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:52294600-52302800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:52295800-52303000	Weak transcription	Brain Anterior Caudate	brain
15	chr5:52297600-52301000	Strong transcription	Hela-S3	cervix
16	chr5:52297600-52301600	Weak transcription	Brain Angular Gyrus	brain
17	chr5:52297600-52301600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:52297800-52301600	Weak transcription	Brain Substantia Nigra	brain
19	chr5:52298400-52301600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr5:52298400-52301800	Genic enhancers	NHEK	skin
21	chr5:52298800-52301400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:52298800-52302800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:52298800-52303400	Enhancers	Dnd41	blood
24	chr5:52299000-52300600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:52299000-52302000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:52299000-52302400	Genic enhancers	HMEC	breast
27	chr5:52299000-52304800	Genic enhancers	HepG2	liver
28	chr5:52299200-52302000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr5:52299200-52302800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:52299400-52300600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:52299400-52313400	Weak transcription	Esophagus	oesophagus
32	chr5:52299600-52300600	Enhancers	HUVEC	blood vessel
33	chr5:52299800-52301400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:52299800-52301800	Enhancers	NHDF-Ad	bronchial
35	chr5:52299800-52302000	Enhancers	NH-A	brain
36	chr5:52299800-52305000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr5:52299800-52306000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:52300000-52302000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:52300000-52302600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:52300200-52300400	Genic enhancers	Brain Hippocampus Middle	brain
41	chr5:52300200-52301000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:52300200-52301000	Enhancers	NHLF	lung
43	chr5:52300200-52301000	Enhancers	Osteobl	bone
44	chr5:52300200-52301200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr5:52300200-52301200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:52300200-52302800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr5:52300200-52303200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:52300200-52304800	Weak transcription	Fetal Intestine Large	intestine
49	chr5:52300200-52305200	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links