Variant report

Variant	rs3733880
Chromosome Location	chr5:52285510-52285511
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:121484544..121485273-chr5:52285389..52286031,2	Hela-S3	cervix:
2	chr5:52260131..52260704-chr5:52285336..52285844,2	MCF-7	breast:
3	chr1:110090680..110091547-chr5:52284624..52285607,2	Hela-S3	cervix:
4	chr3:169491018..169491750-chr5:52284853..52285673,2	Hela-S3	cervix:
5	chr5:52284713..52285560-chr7:107383991..107384708,2	Hela-S3	cervix:
6	chr5:52285298..52286236-chr8:134310006..134310609,2	Hela-S3	cervix:
7	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:
8	chr5:52285098..52285959-chr8:128747992..128748939,2	Hela-S3	cervix:
9	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:
10	chr16:70332608..70333198-chr5:52285135..52286085,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000136997	Chromatin interaction
ENSG00000157349	Chromatin interaction
ENSG00000260537	Chromatin interaction
ENSG00000104419	Chromatin interaction
ENSG00000065135	Chromatin interaction
ENSG00000241764	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000272123	Chromatin interaction
ENSG00000105879	Chromatin interaction
ENSG00000164172	Chromatin interaction
ENSG00000247796	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10038737	0.87[EUR][1000 genomes]
rs10039574	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10052870	0.87[EUR][1000 genomes]
rs13360524	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1421924	0.87[EUR][1000 genomes]
rs16880544	0.87[EUR][1000 genomes]
rs16880552	0.87[EUR][1000 genomes]
rs3928414	0.88[ASN][1000 genomes]
rs41308291	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41311329	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52284000-52288000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:52284200-52286400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:52284200-52286600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:52284400-52285600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:52284400-52285800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr5:52284400-52286200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:52284400-52286200	Active TSS	Sigmoid Colon	Sigmoid Colon
8	chr5:52284400-52286400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr5:52284400-52286400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:52284400-52286400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:52284400-52286600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr5:52284400-52286600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:52284400-52286600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:52284400-52286600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr5:52284400-52286800	Active TSS	Brain Substantia Nigra	brain
16	chr5:52284400-52287000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr5:52284600-52285600	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr5:52284600-52285800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:52284600-52285800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:52284600-52285800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr5:52284600-52285800	Active TSS	Colon Smooth Muscle	Colon
22	chr5:52284600-52285800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
23	chr5:52284600-52285800	Active TSS	Psoas Muscle	Psoas
24	chr5:52284600-52286000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:52284600-52286000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr5:52284600-52286000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
27	chr5:52284600-52286000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:52284600-52286200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:52284600-52286200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:52284600-52286200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr5:52284600-52286200	Active TSS	Gastric	stomach
32	chr5:52284600-52286200	Active TSS	Ovary	ovary
33	chr5:52284600-52286200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr5:52284600-52286400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr5:52284600-52286400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr5:52284600-52286400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:52284600-52286400	Bivalent/Poised TSS	HepG2	liver
38	chr5:52284600-52286600	Active TSS	Brain Cingulate Gyrus	brain
39	chr5:52284600-52286600	Active TSS	Esophagus	oesophagus
40	chr5:52284600-52286600	Active TSS	A549	lung
41	chr5:52284600-52286600	Active TSS	NHDF-Ad	bronchial
42	chr5:52284600-52286800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:52284600-52286800	Active TSS	Fetal Brain Female	brain
44	chr5:52284600-52287200	Active TSS	Fetal Kidney	kidney
45	chr5:52284800-52285600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:52284800-52285600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:52284800-52285600	Flanking Active TSS	Liver	Liver
48	chr5:52284800-52285600	Active TSS	Duodenum Mucosa	Duodenum
49	chr5:52284800-52285600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr5:52284800-52285600	Bivalent/Poised TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links