Variant report

Variant	rs56021041
Chromosome Location	chr2:20581685-20581686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr2:20581135-20581830	ECC-1	luminal epithelium:	n/a	n/a
2	GATA3	chr2:20580949-20581701	MCF-7	breast:	n/a	n/a
3	NR3C1	chr2:20581347-20581687	A549	lung:	n/a	n/a
4	GATA3	chr2:20581015-20581754	MCF-7	breast:	n/a	n/a
5	EP300	chr2:20581065-20581708	MCF-7	breast:	n/a	n/a
6	TCF12	chr2:20580901-20581703	MCF-7	breast:	n/a	n/a
7	NFIC	chr2:20581136-20581850	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr2:20580779-20581805	MCF-7	breast:	n/a	n/a
9	NR3C1	chr2:20581346-20581718	A549	lung:	n/a	n/a
10	KAP1	chr2:20581275-20581783	U2OS	brain:	n/a	n/a
11	SIN3AK20	chr2:20580832-20581822	MCF-7	breast:	n/a	n/a
12	EP300	chr2:20580993-20581696	MCF-7	breast:	n/a	n/a
13	KAP1	chr2:20581179-20581795	HEK293	kidney:	n/a	n/a
14	NR3C1	chr2:20581374-20581709	ECC-1	luminal epithelium:	n/a	n/a
15	NFIC	chr2:20581117-20581890	SK-N-SH	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20549378..20551486-chr2:20579801..20582772,2	MCF-7	breast:
2	chr2:20550569..20551899-chr2:20580797..20581746,5	MCF-7	breast:
3	chr2:20578207..20580776-chr2:20580974..20582727,2	MCF-7	breast:
4	chr2:20577593..20583526-chr2:20584013..20588692,7	MCF-7	breast:
5	chr2:20567812..20569800-chr2:20580748..20582620,2	MCF-7	breast:
6	chr2:20573304..20576530-chr2:20577907..20583085,5	MCF-7	breast:
7	chr2:20580907..20581702-chr2:20674201..20675038,4	MCF-7	breast:
8	chr2:20581268..20583206-chr2:20830863..20833030,2	MCF-7	breast:
9	chr2:20544235..20547228-chr2:20579863..20582540,2	K562	blood:
10	chr2:20580053..20581963-chr2:20645867..20647441,2	MCF-7	breast:
11	chr2:20581393..20584603-chr2:20588898..20591026,3	MCF-7	breast:
12	chr2:20577324..20583172-chr2:20644517..20653341,20	MCF-7	breast:

No data

Variant related genes	Relation type
SLC7A15P	TF binding region
ENSG00000055917	Chromatin interaction
ENSG00000232800	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13383113	1.00[AMR][1000 genomes]
rs34057700	0.89[AMR][1000 genomes]
rs56175611	0.89[AMR][1000 genomes]
rs57753286	0.89[AMR][1000 genomes]
rs61039314	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73214387	0.89[AMR][1000 genomes]
rs73216297	0.89[AMR][1000 genomes]
rs73216299	0.89[AMR][1000 genomes]
rs73218109	0.89[AMR][1000 genomes]
rs73218119	0.89[AMR][1000 genomes]
rs73231458	0.89[AMR][1000 genomes]
rs73231460	0.89[AMR][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	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv581165	chr2:20581058-20616990	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20579200-20582400	Weak transcription	A549	lung
2	chr2:20579200-20582600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:20579200-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:20579200-20583000	Weak transcription	HSMM	muscle
5	chr2:20579200-20583200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:20579200-20585400	Weak transcription	Colonic Mucosa	Colon
7	chr2:20579400-20581800	Weak transcription	Fetal Brain Male	brain
8	chr2:20579400-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:20579400-20584600	Weak transcription	Small Intestine	intestine
10	chr2:20579400-20585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:20579400-20586000	Weak transcription	NHDF-Ad	bronchial
12	chr2:20579400-20586200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:20579400-20586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:20579400-20586400	Weak transcription	Osteobl	bone
15	chr2:20580200-20582000	Enhancers	Brain Substantia Nigra	brain
16	chr2:20580200-20582200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:20580200-20582600	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:20580400-20582000	Enhancers	Brain Hippocampus Middle	brain
19	chr2:20580400-20582800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:20580400-20583200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:20580600-20581800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:20580600-20581800	Enhancers	Brain Germinal Matrix	brain
23	chr2:20580600-20581800	Enhancers	Fetal Lung	lung
24	chr2:20580600-20581800	Enhancers	Placenta	Placenta
25	chr2:20580600-20581800	Enhancers	Fetal Stomach	stomach
26	chr2:20580600-20581800	Enhancers	Ovary	ovary
27	chr2:20580600-20581800	Enhancers	Stomach Smooth Muscle	stomach
28	chr2:20580600-20582000	Enhancers	Fetal Intestine Small	intestine
29	chr2:20580600-20582200	Enhancers	Fetal Intestine Large	intestine
30	chr2:20580600-20582200	Enhancers	Fetal Muscle Leg	muscle
31	chr2:20580800-20581800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:20581000-20581800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr2:20581000-20581800	Enhancers	Brain Angular Gyrus	brain
34	chr2:20581000-20581800	Enhancers	Brain Anterior Caudate	brain
35	chr2:20581000-20581800	Enhancers	Colon Smooth Muscle	Colon
36	chr2:20581000-20581800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:20581000-20581800	Enhancers	Fetal Heart	heart
38	chr2:20581000-20581800	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:20581000-20582000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:20581000-20582600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:20581000-20582600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:20581000-20583400	Enhancers	HepG2	liver
43	chr2:20581200-20581800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:20581200-20581800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:20581200-20581800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:20581200-20581800	Enhancers	Liver	Liver
47	chr2:20581200-20582000	Enhancers	Adipose Nuclei	Adipose
48	chr2:20581200-20582600	Enhancers	NHLF	lung
49	chr2:20581200-20583200	Enhancers	Duodenum Mucosa	Duodenum
50	chr2:20581200-20586200	Weak transcription	Fetal Muscle Trunk	muscle

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