Variant report

Variant	rs28715983
Chromosome Location	chr1:94529420-94529421
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	CTCF	chr1:94528710-94529438	A549	lung:	n/a	chr1:94529338-94529356
2	MAFK	chr1:94528956-94529461	IMR90	lung:	n/a	chr1:94529077-94529088 chr1:94529076-94529091
3	RAD21	chr1:94528376-94530003	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr1:94528503-94529443	HCT-116	colon:	n/a	chr1:94529338-94529356
5	CTCF	chr1:94528690-94529478	SK-N-SH	brain:	n/a	chr1:94529338-94529356
6	RAD21	chr1:94528642-94529468	HCT-116	colon:	n/a	n/a
7	SMC3	chr1:94528720-94529549	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr1:94529320-94529470	HUVEC	blood vessel:	n/a	chr1:94529338-94529356
9	MAFK	chr1:94528905-94529472	HepG2	liver:	n/a	chr1:94529077-94529088 chr1:94529076-94529091
10	MAFK	chr1:94528916-94529470	HepG2	liver:	n/a	chr1:94529077-94529088 chr1:94529076-94529091
11	RAD21	chr1:94528695-94529465	HCT-116	colon:	n/a	n/a
12	CTCF	chr1:94529300-94529450	SAEC	small airway:	n/a	chr1:94529338-94529356
13	TEAD4	chr1:94528937-94529449	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94527081..94529532-chr1:94702506..94704195,2	MCF-7	breast:
2	chr1:94528993..94529506-chr1:94706216..94707195,2	MCF-7	breast:
3	chr1:94527833..94529893-chr1:94702894..94705764,2	MCF-7	breast:
4	chr1:94528533..94530442-chr1:94567755..94569846,3	MCF-7	breast:
5	chr1:94502330..94505107-chr1:94527585..94529424,2	MCF-7	breast:

Variant related genes	Relation type
ABCA4	TF binding region
ENSG00000137962	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12759306	0.88[ASN][1000 genomes]
rs1334895	0.88[ASN][1000 genomes]
rs17110991	0.88[ASN][1000 genomes]
rs1931574	0.88[ASN][1000 genomes]
rs57484952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60298190	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871172	chr1:94504545-94535546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv871057	chr1:94513142-94577286	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94521000-94534400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:94522200-94533800	Weak transcription	Aorta	Aorta
3	chr1:94522600-94533200	Weak transcription	Gastric	stomach
4	chr1:94522800-94533400	Weak transcription	Stomach Mucosa	stomach
5	chr1:94523200-94533600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:94523600-94530400	Enhancers	Left Ventricle	heart
7	chr1:94524600-94531200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:94525000-94530600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:94525200-94529600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:94526000-94530200	Enhancers	HUVEC	blood vessel
11	chr1:94526000-94530400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:94526200-94533600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:94526600-94530200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:94526800-94530200	Enhancers	NHDF-Ad	bronchial
15	chr1:94527000-94529800	Enhancers	Osteobl	bone
16	chr1:94527000-94530200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:94527000-94531200	Enhancers	Placenta	Placenta
18	chr1:94527200-94530000	Enhancers	Fetal Heart	heart
19	chr1:94527200-94530000	Enhancers	NHLF	lung
20	chr1:94527400-94529600	Weak transcription	Brain Substantia Nigra	brain
21	chr1:94527400-94530000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:94527600-94529800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:94527600-94532200	Weak transcription	Thymus	Thymus
24	chr1:94527600-94534200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:94527800-94529800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:94527800-94529800	Weak transcription	Spleen	Spleen
27	chr1:94527800-94529800	Enhancers	A549	lung
28	chr1:94527800-94530200	Enhancers	HepG2	liver
29	chr1:94527800-94534400	Weak transcription	HSMMtube	muscle
30	chr1:94528000-94533000	Weak transcription	HMEC	breast
31	chr1:94528000-94533200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:94528000-94533800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:94528000-94534400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:94528200-94533000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:94528600-94530000	Enhancers	Colon Smooth Muscle	Colon
36	chr1:94528600-94530000	Enhancers	Fetal Lung	lung
37	chr1:94528600-94530200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr1:94528600-94530200	Enhancers	Ovary	ovary
39	chr1:94528600-94530400	Enhancers	Adipose Nuclei	Adipose
40	chr1:94528800-94529600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:94528800-94529800	Enhancers	Fetal Muscle Leg	muscle
42	chr1:94528800-94529800	Enhancers	Rectal Smooth Muscle	rectum
43	chr1:94528800-94530000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
44	chr1:94528800-94530000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:94528800-94530200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:94528800-94530600	Enhancers	Fetal Kidney	kidney
47	chr1:94528800-94530600	Enhancers	Fetal Stomach	stomach
48	chr1:94529000-94529600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:94529000-94529800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:94529000-94529800	Weak transcription	Right Ventricle	heart

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