Variant report

Variant	rs1209523
Chromosome Location	chr20:22567942-22567943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr20:22566496-22567946	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr20:22567360-22567966	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr20:22567403-22568005	A549	lung:	n/a	n/a
4	RAD21	chr20:22566975-22567964	HepG2	liver:	n/a	n/a
5	SMC3	chr20:22567180-22567944	HepG2	liver:	n/a	chr20:22567442-22567456
6	ZNF263	chr20:22566921-22568355	HEK293-T-REx	kidney:	n/a	chr20:22567911-22567920
7	MAX	chr20:22567071-22568082	A549	lung:	n/a	n/a
8	RAD21	chr20:22567144-22567951	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr20:22567237-22567978	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr20:22566738-22568139	A549	lung:	n/a	chr20:22567481-22567499 chr20:22567482-22567498
11	SIN3A	chr20:22567746-22567967	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr20:22566973-22568029	A549	lung:	n/a	chr20:22567568-22567576 chr20:22567938-22567958 chr20:22567673-22567693 chr20:22567677-22567690
13	CTCF	chr20:22567680-22567970	A549	lung:	n/a	n/a
14	CTCF	chr20:22567093-22567952	HCT-116	colon:	n/a	chr20:22567481-22567499 chr20:22567482-22567498
15	RAD21	chr20:22567043-22568066	HepG2	liver:	n/a	n/a
16	MAX	chr20:22567168-22568038	A549	lung:	n/a	n/a
17	SUZ12	chr20:22564779-22567986	NT2-D1	testis:	n/a	n/a
18	TCF12	chr20:22563510-22568249	A549	lung:	n/a	chr20:22566208-22566218 chr20:22565506-22565513 chr20:22564334-22564344
19	GABPA	chr20:22567291-22567942	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr20:22567073-22568149	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:22567920-22567970	ProgFib	skin:	n/a
2	chr20:22567920-22567970	IMR90	lung:	fetal
3	chr20:22567920-22567970	HRPEpiC	eye:	n/a
4	chr20:22567920-22567970	HCT-116	colon:	n/a
5	chr20:22567920-22567970	GM12891	blood:	n/a
6	chr20:22567920-22567970	GM12878	blood:	n/a
7	chr20:22567920-22567970	NT2-D1	testis:	n/a
8	chr20:22567920-22567970	HUVEC	blood vessel:	n/a
9	chr20:22567920-22567970	BE2_C	brain:	n/a
10	chr20:22567920-22567970	GM19239	blood:	n/a
11	chr20:22567920-22567970	HCPEpiC	choroid plexus:	n/a
12	chr20:22567920-22567970	U87	brain:	n/a
13	chr20:22567920-22567970	ovcar-3	ovarian:	n/a
14	chr20:22567920-22567970	HRE	kidney:	n/a
15	chr20:22567920-22567970	Hepatocyte	liver:	n/a
16	chr20:22567920-22567970	HepG2	liver:	n/a
17	chr20:22567920-22567970	HCF	heart:	n/a
18	chr20:22567920-22567970	AG04449	skin:	fetal
19	chr20:22567920-22567970	AG10803	skin:	n/a
20	chr20:22567920-22567970	HCM	heart:	n/a
21	chr20:22567920-22567970	NHBE	bronchial:	n/a
22	chr20:22567920-22567970	SK-N-SH	brain:	n/a
23	chr20:22567920-22567970	RPTEC	kidney:	n/a
24	chr20:22567920-22567970	NHDF-neo	bronchial:	n/a
25	chr20:22567920-22567970	H1-hESC	embryonic stem cell:	embryo
26	chr20:22567920-22567970	LNCaP	prostate:	n/a
27	chr20:22567920-22567970	AoSMC	blood vessel:	n/a
28	chr20:22567920-22567970	AG04450	lung:	fetal
29	chr20:22567920-22567970	SAEC	small airway:	n/a
30	chr20:22567920-22567970	Caco-2	colon:	n/a
31	chr20:22567920-22567970	SK-N-SH_RA	brain:	n/a
32	chr20:22567920-22567970	ECC-1	luminal epithelium:	n/a
33	chr20:22567920-22567970	SKMC	muscle:	n/a
34	chr20:22567920-22567970	HL-60	blood:	n/a
35	chr20:22567920-22567970	PANC-1	pancreas:	n/a
36	chr20:22567920-22567970	HMEC	breast:	n/a
37	chr20:22567920-22567970	HEEpiC	esophagus:	n/a
38	chr20:22567920-22567970	K562	blood:	n/a
39	chr20:22567920-22567970	CMK	blood:	n/a
40	chr20:22567920-22567970	HPAEpiC	pulmonary alveolar:	n/a
41	chr20:22567920-22567970	AG09319	gingival:	n/a
42	chr20:22567920-22567970	MCF10A-Er-Src	breast:	n/a
43	chr20:22567920-22567970	PrEC	prostate:	n/a
44	chr20:22567920-22567970	SK-N-MC	brain:	n/a
45	chr20:22567920-22567970	GM06990	blood:	n/a
46	chr20:22567920-22567970	HIPEpiC	eye:	n/a
47	chr20:22567920-22567970	GM12892	blood:	n/a
48	chr20:22567920-22567970	A549	lung:	n/a
49	chr20:22567920-22567970	HNPCEpiC	eye:	n/a
50	chr20:22567920-22567970	MCF-7	breast:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:22319446..22320369-chr20:22567291..22568037,4	MCF-7	breast:
2	chr20:22563678..22565850-chr20:22566909..22570502,3	K562	blood:
3	chr20:22366314..22367169-chr20:22567127..22567944,2	K562	blood:
4	chr20:22319372..22320425-chr20:22567034..22567962,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA2-1	chr20:22567875-22568426	XLOC_013685

No data

Variant related genes	Relation type
FOXA2	TF binding region
FOXA2	CpG island
ENSG00000125798	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1055080	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1203884	0.87[TSI][hapmap]
rs1203898	0.81[EUR][1000 genomes]
rs1203899	0.81[ASN][1000 genomes]
rs1203902	0.86[ASN][1000 genomes]
rs1203905	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1203907	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1203910	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203915	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203918	0.90[ASN][1000 genomes]
rs1203919	0.89[ASN][1000 genomes]
rs1337918	0.98[EUR][1000 genomes]
rs1337919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs1337920	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1337921	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800847	0.89[EUR][1000 genomes]
rs1974	0.82[EUR][1000 genomes]
rs2277764	0.96[EUR][1000 genomes]
rs6048205	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6048206	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6048209	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs8123991	0.95[EUR][1000 genomes]
rs910958	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428690	chr20:22528757-22649625	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Fasting plasma glucose	20152958	GWAS catalog

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22567000-22568000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:22567200-22568000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr20:22567200-22568000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr20:22567200-22568000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:22567200-22568000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr20:22567400-22568000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:22567400-22568000	Active TSS	Liver	Liver
8	chr20:22567400-22568000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
9	chr20:22567400-22568000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr20:22567400-22568000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
11	chr20:22567400-22568200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr20:22567600-22568000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr20:22567600-22568000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr20:22567600-22568000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr20:22567600-22568000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr20:22567600-22568000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
17	chr20:22567600-22568200	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr20:22567800-22568000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr20:22567800-22568000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:22567800-22568000	Bivalent Enhancer	Adipose Nuclei	Adipose
21	chr20:22567800-22568000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
22	chr20:22567800-22568000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
23	chr20:22567800-22568000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
24	chr20:22567800-22568000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr20:22567800-22568000	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr20:22567800-22568000	Flanking Active TSS	Pancreas	Pancrea
27	chr20:22567800-22568000	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
28	chr20:22567800-22568200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr20:22567800-22568200	Flanking Active TSS	A549	lung

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