Variant report

Variant	rs60420728
Chromosome Location	chr5:146614940-146614941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:146614183-146615139	H1-neurons	neurons:	n/a	n/a
2	RAD21	chr5:146614186-146615035	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:146614236-146615309	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr5:146614403-146615026	H1-hESC	embryonic stem cell:	n/a	chr5:146614948-146614959 chr5:146614951-146614962 chr5:146614950-146614958
5	CHD1	chr5:146614811-146614959	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr5:146614908-146615226	A549	lung:	n/a	chr5:146615069-146615080
7	CEBPB	chr5:146614929-146615150	MCF-7	breast:	n/a	chr5:146615069-146615080
8	REST	chr5:146613995-146615341	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr5:146614201-146615144	H1-neurons	neurons:	n/a	n/a
10	FOS	chr5:146614940-146615108	MCF10A-Er-Src	breast:	n/a	chr5:146614948-146614959 chr5:146614951-146614962 chr5:146614950-146614958
11	CEBPB	chr5:146614888-146615227	HepG2	liver:	n/a	chr5:146615069-146615080
12	TAF1	chr5:146614299-146615044	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr5:146614873-146615232	H1-hESC	embryonic stem cell:	n/a	chr5:146615069-146615080

Variant related genes	Relation type
ENSG00000250343	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs58255109	0.89[AFR][1000 genomes]
rs58411748	0.89[AFR][1000 genomes]
rs73326961	0.98[AFR][1000 genomes]
rs73326965	0.89[AFR][1000 genomes]
rs73327002	0.89[AFR][1000 genomes]
rs73328904	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv883014	chr5:146557552-146615260	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146613400-146615200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:146613400-146615200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr5:146613400-146616000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:146613600-146615000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:146613600-146615000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:146613600-146615000	Active TSS	Aorta	Aorta
7	chr5:146613600-146615000	Active TSS	Psoas Muscle	Psoas
8	chr5:146613600-146615000	Bivalent/Poised TSS	Osteobl	bone
9	chr5:146613600-146615200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr5:146613600-146615200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr5:146613600-146615200	Active TSS	Brain Anterior Caudate	brain
12	chr5:146613600-146615200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
13	chr5:146613600-146615200	Active TSS	Brain Substantia Nigra	brain
14	chr5:146613600-146615200	Active TSS	Right Atrium	heart
15	chr5:146613600-146615400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr5:146613600-146615400	Bivalent/Poised TSS	Fetal Kidney	kidney
17	chr5:146613600-146616000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:146613800-146615000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:146613800-146615000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:146613800-146615000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:146613800-146615000	Bivalent Enhancer	Liver	Liver
22	chr5:146613800-146615200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr5:146614000-146615000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:146614000-146615000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr5:146614000-146615000	Active TSS	Right Ventricle	heart
26	chr5:146614000-146615200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:146614200-146615000	Flanking Active TSS	HMEC	breast
28	chr5:146614200-146615200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:146614400-146615000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr5:146614400-146615200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:146614400-146615800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:146614400-146617800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:146614600-146615000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr5:146614600-146615000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
35	chr5:146614600-146615000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:146614600-146615000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr5:146614600-146615000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
38	chr5:146614600-146615000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:146614600-146615000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
40	chr5:146614600-146615000	Bivalent Enhancer	Small Intestine	intestine
41	chr5:146614600-146615000	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
42	chr5:146614600-146615000	Bivalent/Poised TSS	NHEK	skin
43	chr5:146614600-146615200	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr5:146614600-146615200	Bivalent Enhancer	Fetal Heart	heart
45	chr5:146614600-146615200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
46	chr5:146614600-146615400	Bivalent/Poised TSS	Fetal Brain Male	brain
47	chr5:146614800-146615000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
48	chr5:146614800-146615000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:146614800-146615000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
50	chr5:146614800-146615000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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