Variant report

Variant	rs2424580
Chromosome Location	chr20:23619543-23619544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:23619525-23619575	HCF	heart:	n/a
2	chr20:23619525-23619575	ovcar-3	ovarian:	n/a
3	chr20:23619525-23619575	AG09319	gingival:	n/a
4	chr20:23619525-23619575	Hepatocyte	liver:	n/a
5	chr20:23619525-23619575	MCF10A-Er-Src	breast:	n/a
6	chr20:23619525-23619575	AG04450	lung:	fetal
7	chr20:23619525-23619575	NB4	blood:	n/a
8	chr20:23619525-23619575	NHDF-neo	bronchial:	n/a
9	chr20:23619525-23619575	HRCEpiC	kidney:	n/a
10	chr20:23619525-23619575	IMR90	lung:	fetal
11	chr20:23619525-23619575	AG04449	skin:	fetal
12	chr20:23619525-23619575	SK-N-SH	brain:	n/a
13	chr20:23619525-23619575	HEEpiC	esophagus:	n/a
14	chr20:23619525-23619575	RPTEC	kidney:	n/a
15	chr20:23619525-23619575	HEK293	kidney:	embryo
16	chr20:23619525-23619575	AoSMC	blood vessel:	n/a
17	chr20:23619525-23619575	HMEC	breast:	n/a
18	chr20:23619525-23619575	ProgFib	skin:	n/a
19	chr20:23619525-23619575	HRPEpiC	eye:	n/a
20	chr20:23619525-23619575	H1-hESC	embryonic stem cell:	embryo
21	chr20:23619525-23619575	Jurkat	blood:	n/a
22	chr20:23619525-23619575	A549	lung:	n/a
23	chr20:23619525-23619575	NHBE	bronchial:	n/a
24	chr20:23619525-23619575	HNPCEpiC	eye:	n/a
25	chr20:23619525-23619575	Hela-S3	cervix:	n/a
26	chr20:23619525-23619575	SK-N-MC	brain:	n/a
27	chr20:23619525-23619575	PrEC	prostate:	n/a
28	chr20:23619525-23619575	GM12878	blood:	n/a
29	chr20:23619525-23619575	HCM	heart:	n/a
30	chr20:23619525-23619575	HAEpiC	amniotic membrane:	n/a
31	chr20:23619525-23619575	SK-N-SH_RA	brain:	n/a
32	chr20:23619525-23619575	GM19239	blood:	n/a
33	chr20:23619525-23619575	BJ	skin:	n/a
34	chr20:23619525-23619575	AG09309	skin:	n/a
35	chr20:23619525-23619575	PANC-1	pancreas:	n/a
36	chr20:23619525-23619575	LNCaP	prostate:	n/a
37	chr20:23619525-23619575	GM06990	blood:	n/a
38	chr20:23619525-23619575	HCPEpiC	choroid plexus:	n/a
39	chr20:23619525-23619575	HPAEpiC	pulmonary alveolar:	n/a
40	chr20:23619525-23619575	HCT-116	colon:	n/a
41	chr20:23619525-23619575	HUVEC	blood vessel:	n/a
42	chr20:23619525-23619575	GM12892	blood:	n/a
43	chr20:23619525-23619575	K562	blood:	n/a
44	chr20:23619525-23619575	U87	brain:	n/a
45	chr20:23619525-23619575	SKMC	muscle:	n/a
46	chr20:23619525-23619575	ECC-1	luminal epithelium:	n/a
47	chr20:23619525-23619575	MCF-7	breast:	n/a
48	chr20:23619525-23619575	SAEC	small airway:	n/a
49	chr20:23619525-23619575	HL-60	blood:	n/a
50	chr20:23619525-23619575	T-47D	breast:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23400787..23402892-chr20:23617355..23620191,2	MCF-7	breast:
2	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
3	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:

No data

Variant related genes	Relation type
CST3	CpG island
ENSG00000125812	Chromatin interaction
ENSG00000270001	Chromatin interaction
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6138024	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv964381	chr20:23614805-23621846	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	esv3359195	chr20:23617352-23620750	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3377051	chr20:23617777-23620325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3336303	chr20:23617902-23620300	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23619600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr20:23618600-23620000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:23618600-23620000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr20:23618600-23620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:23618600-23620400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr20:23618600-23620800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:23618600-23621000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr20:23618600-23621200	Weak transcription	Ovary	ovary
9	chr20:23618600-23621200	Weak transcription	GM12878-XiMat	blood
10	chr20:23618600-23621600	Weak transcription	Liver	Liver
11	chr20:23618600-23621600	Weak transcription	Brain Hippocampus Middle	brain
12	chr20:23618600-23621800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:23618600-23621800	Weak transcription	Left Ventricle	heart
14	chr20:23618600-23622000	Weak transcription	HUVEC	blood vessel
15	chr20:23618600-23622200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr20:23618600-23622400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr20:23618600-23622400	Weak transcription	NHDF-Ad	bronchial
18	chr20:23618600-23622400	Weak transcription	NHLF	lung
19	chr20:23618600-23622600	Weak transcription	Brain Anterior Caudate	brain
20	chr20:23618600-23622600	Weak transcription	Brain Substantia Nigra	brain
21	chr20:23618600-23622600	Weak transcription	Colon Smooth Muscle	Colon
22	chr20:23618600-23624800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr20:23618600-23626000	Weak transcription	Gastric	stomach
24	chr20:23618800-23619600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:23618800-23619600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr20:23618800-23619600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr20:23618800-23619600	Enhancers	Adipose Nuclei	Adipose
28	chr20:23618800-23619800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr20:23618800-23620000	Enhancers	NHEK	skin
30	chr20:23618800-23620400	Enhancers	A549	lung
31	chr20:23618800-23620600	Weak transcription	Fetal Intestine Large	intestine
32	chr20:23618800-23620800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr20:23618800-23621000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr20:23618800-23621200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr20:23618800-23621200	Weak transcription	Psoas Muscle	Psoas
36	chr20:23618800-23621400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr20:23618800-23621400	Weak transcription	Primary B cells from cord blood	blood
38	chr20:23618800-23621400	Weak transcription	HSMMtube	muscle
39	chr20:23618800-23621600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr20:23618800-23621600	Weak transcription	Pancreas	Pancrea
41	chr20:23618800-23621600	Weak transcription	HSMM	muscle
42	chr20:23618800-23621800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr20:23618800-23622000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:23618800-23622000	Enhancers	Placenta	Placenta
45	chr20:23618800-23622000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr20:23618800-23622200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr20:23618800-23622400	Weak transcription	Fetal Lung	lung
48	chr20:23618800-23622400	Weak transcription	Osteobl	bone
49	chr20:23618800-23622600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr20:23618800-23622600	Weak transcription	Right Atrium	heart

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