Variant report

Variant	rs28558979
Chromosome Location	chr5:68820348-68820349
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68787211..68792044-chr5:68819088..68825852,9	MCF-7	breast:
2	chr5:68820102..68821620-chr5:68821807..68823888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs256914	0.83[ASN][1000 genomes]
rs28404493	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28407209	0.87[AMR][1000 genomes]
rs28431145	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28489109	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28513225	0.85[AMR][1000 genomes]
rs28531719	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28552895	0.88[ASN][1000 genomes]
rs28562181	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612873	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28633210	0.84[ASN][1000 genomes]
rs28807720	0.85[ASN][1000 genomes]
rs3733742	0.84[AMR][1000 genomes]
rs3806856	0.85[AMR][1000 genomes]
rs3846487	0.81[AMR][1000 genomes]
rs55923832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	esv1804444	chr5:68812530-68838432	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv1818827	chr5:68812530-68849594	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv1832055	chr5:68812530-68849594	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv1830977	chr5:68815501-68850642	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28558979	GUSBP3	cis	Whole Blood	GTEx

Chromatin state (count:37 , 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	chr5:68799000-68823200	Weak transcription	Placenta	Placenta
3	chr5:68799400-68821800	Weak transcription	Fetal Stomach	stomach
4	chr5:68805600-68821600	Weak transcription	Lung	lung
5	chr5:68805600-68823400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:68805600-68826200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:68805600-68826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:68806000-68824200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:68806400-68826400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:68806800-68821400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:68807000-68821400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:68807000-68821600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:68810400-68821600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:68810400-68821800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:68810400-68823600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:68814000-68823400	Weak transcription	Fetal Lung	lung
17	chr5:68814400-68823600	Weak transcription	Small Intestine	intestine
18	chr5:68814600-68822000	Weak transcription	Fetal Kidney	kidney
19	chr5:68815400-68826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:68815800-68831000	Weak transcription	HepG2	liver
21	chr5:68816000-68821600	Weak transcription	Liver	Liver
22	chr5:68816000-68821600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:68816800-68822600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:68817000-68821600	Weak transcription	Pancreas	Pancrea
25	chr5:68817200-68827200	Weak transcription	GM12878-XiMat	blood
26	chr5:68817400-68823400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:68817400-68823400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:68817600-68821600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:68818000-68820600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:68818000-68821600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:68818000-68821600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:68818000-68821600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:68818000-68823000	Weak transcription	Stomach Mucosa	stomach
34	chr5:68818600-68821400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:68819000-68821600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:68819800-68824600	Genic enhancers	Fetal Intestine Small	intestine
37	chr5:68820200-68820600	Enhancers	Fetal Intestine Large	intestine

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