Variant report

Variant	rs2424592
Chromosome Location	chr20:23638021-23638022
allele	G/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	MAX	chr20:23637796-23638245	HCT-116	colon:	n/a	chr20:23637967-23637974
2	CTCF	chr20:23637921-23638143	HepG2	liver:	n/a	n/a
3	MYC	chr20:23637910-23638149	MCF-7	breast:	n/a	chr20:23637967-23637974
4	CTCF	chr20:23637952-23638112	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr20:23637858-23638194	HepG2	liver:	n/a	n/a
6	MYC	chr20:23637998-23638083	MCF-7	breast:	n/a	n/a
7	MYC	chr20:23637992-23638045	MCF-7	breast:	n/a	n/a
8	CTCF	chr20:23637880-23638030	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr20:23637922-23638137	MCF-7	breast:	n/a	n/a
10	RAD21	chr20:23637883-23638191	HepG2	liver:	n/a	n/a
11	CTCF	chr20:23637960-23638110	WERI-Rb-1	eye:	n/a	n/a
12	MAX	chr20:23637737-23638203	HCT-116	colon:	n/a	chr20:23637967-23637974
13	CTCF	chr20:23637940-23638090	HCT-116	colon:	n/a	n/a
14	CTCF	chr20:23637969-23638070	GM12892	blood:	n/a	n/a
15	CTCF	chr20:23637924-23638147	MCF-7	breast:	n/a	n/a
16	CTCF	chr20:23637980-23638130	HepG2	liver:	n/a	n/a
17	CTCF	chr20:23637964-23638070	Hela-S3	cervix:	n/a	n/a
18	MYC	chr20:23637949-23638100	MCF-7	breast:	n/a	chr20:23637967-23637974
19	CTCF	chr20:23637982-23638048	HepG2	liver:	n/a	n/a
20	CTCF	chr20:23637916-23638146	MCF-7	breast:	n/a	n/a
21	MAFF	chr20:23637959-23638448	HepG2	liver:	n/a	chr20:23638327-23638341 chr20:23638321-23638339
22	CTCF	chr20:23637913-23638143	MCF-7	breast:	n/a	n/a
23	RAD21	chr20:23637848-23638189	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr20:23637902-23638152	MCF-7	breast:	n/a	n/a
25	CTCF	chr20:23637961-23638084	Pancreas_OC	pancreas:	n/a	n/a
26	CTCF	chr20:23637920-23638070	HCT-116	colon:	n/a	n/a
27	POLR2A	chr20:23638015-23638112	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000225056	TF binding region

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2424589	0.80[AMR][1000 genomes]
rs2424596	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424597	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048980	0.82[EUR][1000 genomes]
rs6048981	0.81[EUR][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	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
2	chr20:23633000-23639400	Enhancers	HepG2	liver
3	chr20:23634800-23638400	Weak transcription	Fetal Intestine Small	intestine
4	chr20:23635600-23641600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr20:23636200-23638200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:23636600-23638200	Enhancers	Pancreas	Pancrea
7	chr20:23636800-23638600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:23636800-23640600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr20:23636800-23640800	Weak transcription	Aorta	Aorta
10	chr20:23637000-23638200	Enhancers	Adipose Nuclei	Adipose
11	chr20:23637000-23639200	Weak transcription	Psoas Muscle	Psoas
12	chr20:23637000-23640600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr20:23637200-23638600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr20:23637200-23638600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr20:23637200-23639000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr20:23637200-23640000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr20:23637200-23640600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:23637200-23640800	Weak transcription	Fetal Muscle Leg	muscle
19	chr20:23637200-23641000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:23637200-23641600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr20:23637200-23643600	Weak transcription	Right Atrium	heart
22	chr20:23637200-23660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:23637400-23638600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr20:23637400-23639000	Weak transcription	Fetal Lung	lung
25	chr20:23637400-23639400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:23637400-23640800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr20:23637400-23641000	Weak transcription	Esophagus	oesophagus
28	chr20:23637600-23638200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr20:23637800-23638200	Enhancers	Brain Hippocampus Middle	brain
30	chr20:23637800-23644200	Enhancers	Fetal Intestine Large	intestine
31	chr20:23638000-23638200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr20:23638000-23638800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr20:23638000-23640200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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