Variant report

Variant	rs28404493
Chromosome Location	chr5:68807417-68807418
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68798653..68800234-chr5:68805143..68807685,2	MCF-7	breast:
2	chr5:68805354..68807597-chr5:68808113..68809908,2	MCF-7	breast:
3	chr5:68781306..68783757-chr5:68806560..68809193,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197822	Chromatin interaction
ENSG00000249295	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs256914	0.81[ASN][1000 genomes]
rs28407209	0.87[AMR][1000 genomes]
rs28431145	0.93[ASN][1000 genomes]
rs28489109	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513225	0.85[AMR][1000 genomes]
rs28531719	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28552895	0.85[ASN][1000 genomes]
rs28558979	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28562181	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28612873	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28633210	0.85[ASN][1000 genomes]
rs28807720	0.88[ASN][1000 genomes]
rs3733742	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3806856	0.85[AMR][1000 genomes]
rs3846487	0.81[AMR][1000 genomes]
rs55923832	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28404493	GUSBP3	cis	Whole Blood	GTEx
rs28404493	GTF2H2,GTF2H2B,GTF2H2C,GTF2H2D	cis	brain	BrainEAC

Chromatin state (count:47 , 50 per page) page: 1

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	chr5:68799000-68808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:68799000-68823200	Weak transcription	Placenta	Placenta
5	chr5:68799200-68808200	Weak transcription	Stomach Mucosa	stomach
6	chr5:68799400-68808200	Weak transcription	Small Intestine	intestine
7	chr5:68799400-68808200	Weak transcription	HUVEC	blood vessel
8	chr5:68799400-68808600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:68799400-68814200	Weak transcription	Colonic Mucosa	Colon
10	chr5:68799400-68821800	Weak transcription	Fetal Stomach	stomach
11	chr5:68799800-68809000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:68800000-68807800	Strong transcription	Fetal Intestine Small	intestine
13	chr5:68800000-68808200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:68800000-68808800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:68800200-68808200	Weak transcription	A549	lung
16	chr5:68802200-68808800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:68802400-68808800	Weak transcription	Gastric	stomach
18	chr5:68804000-68809600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:68805400-68812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:68805400-68813000	Weak transcription	Esophagus	oesophagus
21	chr5:68805600-68808800	Weak transcription	Pancreas	Pancrea
22	chr5:68805600-68816400	Weak transcription	GM12878-XiMat	blood
23	chr5:68805600-68821600	Weak transcription	Lung	lung
24	chr5:68805600-68823400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:68805600-68826200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:68805600-68826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:68806000-68824200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:68806200-68808200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:68806200-68808800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr5:68806200-68808800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:68806400-68808600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:68806400-68826400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:68806800-68808000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:68806800-68808200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:68806800-68808200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:68806800-68808200	Weak transcription	Fetal Intestine Large	intestine
37	chr5:68806800-68808800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:68806800-68808800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:68806800-68809200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:68806800-68809600	Weak transcription	HepG2	liver
41	chr5:68806800-68816800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:68806800-68821400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:68807000-68809000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:68807000-68809200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:68807000-68821400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:68807000-68821600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:68807400-68807600	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links