Variant report

Variant	rs28513225
Chromosome Location	chr5:68788813-68788814
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68388349..68391314-chr5:68786934..68789626,2	MCF-7	breast:
2	chr5:68709515..68715463-chr5:68785927..68791978,14	MCF-7	breast:
3	chr5:68714328..68717643-chr5:68787118..68789259,3	MCF-7	breast:
4	chr5:68710929..68711657-chr5:68788195..68788888,3	MCF-7	breast:
5	chr5:68664038..68667254-chr5:68786797..68789724,5	MCF-7	breast:
6	chr5:68787536..68790695-chr5:68794621..68799046,5	MCF-7	breast:
7	chr5:68780984..68783227-chr5:68787002..68789520,2	MCF-7	breast:
8	chr5:68786861..68791714-chr5:68792845..68799561,13	MCF-7	breast:
9	chr5:68785201..68788163-chr5:68788393..68790569,2	MCF-7	breast:
10	chr5:68708231..68714128-chr5:68786986..68792913,14	MCF-7	breast:
11	chr5:68786843..68790127-chr5:68821932..68828319,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197822	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000212260	Chromatin interaction
ENSG00000249295	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000152939	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10067619	0.85[ASN][1000 genomes]
rs28404493	0.85[AMR][1000 genomes]
rs28407209	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429739	0.86[ASN][1000 genomes]
rs28489109	0.88[AMR][1000 genomes]
rs28531719	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28558979	0.85[AMR][1000 genomes]
rs28562181	0.85[AMR][1000 genomes]
rs28579732	0.88[ASN][1000 genomes]
rs28612873	0.85[AMR][1000 genomes]
rs3733742	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806856	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846487	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923832	0.85[AMR][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
rs28513225	GUSBP3	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68787400-68789000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr5:68787400-68791200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:68787600-68789800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr5:68787600-68790200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr5:68787600-68790200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:68787600-68790400	Active TSS	GM12878-XiMat	blood
7	chr5:68787600-68790600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr5:68787600-68790600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:68787600-68790800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:68787800-68789000	Bivalent/Poised TSS	Fetal Brain Female	brain
11	chr5:68787800-68789000	Bivalent/Poised TSS	Fetal Lung	lung
12	chr5:68787800-68789200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:68787800-68789200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:68787800-68789400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
15	chr5:68787800-68789800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr5:68787800-68789800	Active TSS	Brain Anterior Caudate	brain
17	chr5:68787800-68789800	Active TSS	Duodenum Mucosa	Duodenum
18	chr5:68787800-68789800	Active TSS	Fetal Kidney	kidney
19	chr5:68787800-68790000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:68787800-68790000	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:68787800-68790000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:68787800-68790000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
23	chr5:68787800-68790000	Active TSS	Brain Hippocampus Middle	brain
24	chr5:68787800-68790000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
25	chr5:68787800-68790000	Bivalent/Poised TSS	Small Intestine	intestine
26	chr5:68787800-68790400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:68787800-68790600	Active TSS	Pancreas	Pancrea
28	chr5:68787800-68791400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr5:68788000-68789000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr5:68788000-68789000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
31	chr5:68788000-68789000	Bivalent/Poised TSS	NHEK	skin
32	chr5:68788000-68789200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:68788000-68789400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:68788000-68789400	Active TSS	Hela-S3	cervix
35	chr5:68788000-68789400	Bivalent/Poised TSS	HSMM	muscle
36	chr5:68788000-68789400	Flanking Bivalent TSS/Enh	Osteobl	bone
37	chr5:68788000-68789600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
38	chr5:68788000-68789800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:68788000-68789800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:68788000-68789800	Bivalent Enhancer	Fetal Brain Male	brain
41	chr5:68788000-68790000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:68788000-68790000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
44	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr5:68788000-68790000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach

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