Variant report

Variant	rs1072389
Chromosome Location	chr4:74999784-74999785
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:74903212..74905934-chr4:74998158..75001243,4	K562	blood:
2	chr4:74605276..74607483-chr4:74998559..75001335,2	MCF-7	breast:
3	chr4:74528172..74529508-chr4:74999705..75000610,7	K562	blood:
4	chr4:74963512..74965298-chr4:74998131..75000514,2	K562	blood:
5	chr4:74595014..74595945-chr4:74999595..75000244,2	MCF-7	breast:
6	chr4:74526162..74527919-chr4:74999556..75002454,2	K562	blood:
7	chr4:74999598..75001723-chr4:75011238..75014051,2	K562	blood:
8	chr4:74388912..74389524-chr4:74999547..75000220,2	MCF-7	breast:
9	chr4:74998740..75001079-chr4:75031773..75033857,2	K562	blood:
10	chr4:74528313..74529074-chr4:74999580..75000552,2	MCF-7	breast:
11	chr4:73933047..73934881-chr4:74998763..75001589,2	K562	blood:
12	chr4:74439365..74440079-chr4:74999743..75000601,2	MCF-7	breast:
13	chr4:74918435..74920620-chr4:74998592..75000975,2	K562	blood:
14	chr4:74589150..74590025-chr4:74999644..75000508,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000081041	Chromatin interaction
ENSG00000163734	Chromatin interaction
ENSG00000248848	Chromatin interaction
ENSG00000169429	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3775488	1.00[YRI][hapmap]
rs491641	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7660423	0.83[MKK][hapmap]

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	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1072389	CCNG2	cis	parietal	SCAN
rs1072389	UTP3	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74998600-75000000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:74998600-75000000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:74998800-74999800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:74998800-75000000	Enhancers	Brain Anterior Caudate	brain
5	chr4:74998800-75000000	Enhancers	Brain Substantia Nigra	brain
6	chr4:74998800-75000200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:74998800-75000200	Enhancers	Brain Hippocampus Middle	brain
8	chr4:74999000-75000000	Enhancers	Liver	Liver
9	chr4:74999000-75000200	Enhancers	HMEC	breast
10	chr4:74999200-75002200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:74999400-75000000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:74999400-75000200	Enhancers	Brain Angular Gyrus	brain
13	chr4:74999400-75000200	Enhancers	Brain Cingulate Gyrus	brain
14	chr4:74999600-75000000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:74999600-75000000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:74999600-75000000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr4:74999600-75000000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:74999600-75000000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:74999600-75000000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:74999600-75000000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:74999600-75000000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr4:74999600-75000000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:74999600-75000000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr4:74999600-75000000	Enhancers	Fetal Thymus	thymus
25	chr4:74999600-75000000	Enhancers	Dnd41	blood
26	chr4:74999600-75000000	Enhancers	HUVEC	blood vessel
27	chr4:74999600-75000000	Enhancers	NHLF	lung
28	chr4:74999600-75000000	Enhancers	Osteobl	bone
29	chr4:74999600-75000200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr4:74999600-75000200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:74999600-75000200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:74999600-75000200	Enhancers	Left Ventricle	heart
33	chr4:74999600-75000200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr4:74999600-75000200	Enhancers	Right Atrium	heart
35	chr4:74999600-75000200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr4:74999600-75000200	Enhancers	Hela-S3	cervix
37	chr4:74999600-75000200	Enhancers	HSMM	muscle
38	chr4:74999600-75000200	Genic enhancers	NHEK	skin
39	chr4:74999600-75000400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:74999600-75000400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:74999600-75000400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:74999600-75000400	Enhancers	K562	blood
43	chr4:74999600-75000600	Enhancers	NHDF-Ad	bronchial

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