Variant report

Variant	rs28489109
Chromosome Location	chr5:68808501-68808502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68788289..68790354-chr5:68807453..68809704,2	MCF-7	breast:
2	chr5:68808067..68811530-chr5:68811540..68813490,3	MCF-7	breast:
3	chr5:68781306..68783757-chr5:68806560..68809193,2	MCF-7	breast:
4	chr5:68805354..68807597-chr5:68808113..68809908,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249295	Chromatin interaction
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs256914	0.81[ASN][1000 genomes]
rs28404493	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28407209	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28431145	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28513225	0.88[AMR][1000 genomes]
rs28531719	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28552895	0.85[ASN][1000 genomes]
rs28558979	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28562181	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28612873	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28633210	0.85[ASN][1000 genomes]
rs28807720	0.88[ASN][1000 genomes]
rs3733742	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3806856	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3846487	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55923832	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1023116	chr5:68744307-68867282	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1034024	chr5:68760271-69118123	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28489109	GUSBP3	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68790200-68824600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:68793200-68813600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:68799000-68823200	Weak transcription	Placenta	Placenta
4	chr5:68799400-68808600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:68799400-68814200	Weak transcription	Colonic Mucosa	Colon
6	chr5:68799400-68821800	Weak transcription	Fetal Stomach	stomach
7	chr5:68799800-68809000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:68800000-68808800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:68802200-68808800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:68802400-68808800	Weak transcription	Gastric	stomach
11	chr5:68804000-68809600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:68805400-68812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:68805400-68813000	Weak transcription	Esophagus	oesophagus
14	chr5:68805600-68808800	Weak transcription	Pancreas	Pancrea
15	chr5:68805600-68816400	Weak transcription	GM12878-XiMat	blood
16	chr5:68805600-68821600	Weak transcription	Lung	lung
17	chr5:68805600-68823400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:68805600-68826200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:68805600-68826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:68806000-68824200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:68806200-68808800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:68806200-68808800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:68806400-68808600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:68806400-68826400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:68806800-68808800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:68806800-68808800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:68806800-68809200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:68806800-68809600	Weak transcription	HepG2	liver
29	chr5:68806800-68816800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:68806800-68821400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:68807000-68809000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:68807000-68809200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:68807000-68821400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:68807000-68821600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:68807800-68810200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:68808000-68809400	Enhancers	Osteobl	bone
37	chr5:68808000-68809600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr5:68808000-68809600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:68808000-68809600	Enhancers	NH-A	brain
40	chr5:68808000-68809600	Enhancers	NHDF-Ad	bronchial
41	chr5:68808000-68810200	Enhancers	Liver	Liver
42	chr5:68808000-68810400	Enhancers	Fetal Intestine Small	intestine
43	chr5:68808000-68810400	Enhancers	Hela-S3	cervix
44	chr5:68808200-68808600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:68808200-68808800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:68808200-68808800	Enhancers	A549	lung
47	chr5:68808200-68809000	Enhancers	Small Intestine	intestine
48	chr5:68808200-68809200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:68808200-68809200	Enhancers	NHEK	skin
50	chr5:68808200-68809400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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