Variant report

Variant	rs6048794
Chromosome Location	chr20:23402152-23402153
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	TAF1	chr20:23401882-23402285	GM12892	blood:	n/a	n/a
2	MYC	chr20:23401877-23402458	NB4	blood:	n/a	chr20:23401908-23401918
3	RUNX3	chr20:23401852-23402344	GM12878	blood:	n/a	n/a
4	TAF1	chr20:23401870-23402257	H1-hESC	embryonic stem cell:	n/a	n/a
5	USF1	chr20:23402094-23402387	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr20:23401828-23402168	GM12892	blood:	n/a	n/a
7	YY1	chr20:23401879-23402337	K562	blood:	n/a	chr20:23402183-23402192
8	POLR2A	chr20:23401715-23402435	ProgFib	skin:	n/a	n/a
9	CTCF	chr20:23402019-23402174	ProgFib	skin:	n/a	n/a
10	SIX5	chr20:23402044-23402323	K562	blood:	n/a	chr20:23402210-23402219 chr20:23402157-23402166 chr20:23402159-23402168 chr20:23402208-23402217
11	SIN3AK20	chr20:23401858-23402180	K562	blood:	n/a	n/a
12	RCOR1	chr20:23401969-23402426	K562	blood:	n/a	n/a
13	POLR2A	chr20:23401755-23402439	A549	lung:	n/a	n/a
14	CTCF	chr20:23402080-23402230	GM12865	blood:	n/a	n/a
15	NFIC	chr20:23401843-23402504	HepG2	liver:	n/a	n/a
16	TAF1	chr20:23401916-23402280	K562	blood:	n/a	n/a
17	ELF1	chr20:23401459-23402368	GM12878	blood:	n/a	n/a
18	MYBL2	chr20:23401743-23402580	HepG2	liver:	n/a	n/a
19	YY1	chr20:23401864-23402426	GM12878	blood:	n/a	chr20:23402183-23402192
20	RUNX3	chr20:23401842-23402343	GM12878	blood:	n/a	n/a
21	TEAD4	chr20:23402013-23402377	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr20:23401946-23402406	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr20:23402007-23402183	MCF-7	breast:	n/a	n/a
24	HA-E2F1	chr20:23401819-23402421	MCF-7	breast:	n/a	chr20:23402124-23402133 chr20:23402183-23402192 chr20:23402130-23402139
25	POLR2A	chr20:23401815-23402236	HepG2	liver:	n/a	n/a
26	E2F4	chr20:23402010-23402343	MCF10A-Er-Src	breast:	n/a	chr20:23402124-23402133 chr20:23402183-23402192 chr20:23402130-23402139
27	USF2	chr20:23402051-23402325	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr20:23401903-23402246	H1-neurons	neurons:	n/a	n/a
29	MXI1	chr20:23401931-23402420	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBP	chr20:23401765-23402459	K562	blood:	n/a	n/a
31	CTCF	chr20:23402060-23402210	HEEpiC	esophagus:	n/a	n/a
32	CTCF	chr20:23402080-23402230	AG09309	skin:	n/a	n/a
33	CTCF	chr20:23402040-23402190	A549	lung:	n/a	n/a
34	POLR2A	chr20:23401832-23402269	HUVEC	blood vessel:	n/a	n/a
35	ZBTB7A	chr20:23401008-23402400	K562	blood:	n/a	chr20:23401304-23401312 chr20:23401767-23401776
36	CTCF	chr20:23401904-23402270	H1-hESC	embryonic stem cell:	n/a	n/a
37	SP1	chr20:23401852-23402504	A549	lung:	n/a	chr20:23402230-23402239 chr20:23402228-23402240 chr20:23402229-23402239 chr20:23402230-23402239 chr20:23402228-23402240 chr20:23402229-23402238 chr20:23401904-23401913
38	CTCF	chr20:23402080-23402230	HRPEpiC	eye:	n/a	n/a
39	PML	chr20:23401922-23402218	K562	blood:	n/a	n/a
40	CTCF	chr20:23401685-23402462	IMR90	lung:	n/a	chr20:23401764-23401774 chr20:23401760-23401776 chr20:23401759-23401777 chr20:23401762-23401775
41	TBL1XR1	chr20:23401952-23402426	K562	blood:	n/a	n/a
42	CTCF	chr20:23402026-23402196	GM10266	blood:	n/a	n/a
43	ZBTB7A	chr20:23400884-23402543	K562	blood:	n/a	chr20:23401304-23401312 chr20:23401767-23401776
44	HEY1	chr20:23401760-23402536	HepG2	liver:	n/a	n/a
45	YY1	chr20:23401996-23402346	HCT-116	colon:	n/a	chr20:23402183-23402192
46	POLR2A	chr20:23401835-23402430	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr20:23402040-23402190	HepG2	liver:	n/a	n/a
48	FOXP2	chr20:23401841-23402292	PFSK-1	brain:	n/a	n/a
49	ZBTB7A	chr20:23400929-23402584	ECC-1	luminal epithelium:	n/a	chr20:23401304-23401312 chr20:23401767-23401776
50	POLR2A	chr20:23401809-23402244	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23336395..23338655-chr20:23399846..23402203,2	K562	blood:
2	chr20:23342672..23344892-chr20:23400555..23402881,3	MCF-7	breast:
3	chr20:23337918..23344174-chr20:23400107..23404916,9	MCF-7	breast:
4	chr20:23330877..23333588-chr20:23399396..23402604,5	K562	blood:
5	chr20:23338809..23345308-chr20:23399768..23403114,12	K562	blood:
6	chr20:23402152..23403758-chr20:23404630..23407146,2	K562	blood:
7	chr20:23340976..23344072-chr20:23400128..23403114,5	K562	blood:
8	chr20:23400310..23402508-chr20:23615661..23618868,3	MCF-7	breast:
9	chr20:23345633..23349899-chr20:23400854..23404181,4	K562	blood:
10	chr20:23400787..23402892-chr20:23617355..23620191,2	MCF-7	breast:
11	chr20:23345633..23349899-chr20:23400647..23404181,5	K562	blood:

Variant related genes	Relation type
NAPB	TF binding region
ENSG00000132661	Chromatin interaction
ENSG00000234832	Chromatin interaction
ENSG00000125812	Chromatin interaction
ENSG00000101439	Chromatin interaction
ENSG00000232645	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11908625	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1203994	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2281433	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036393	0.83[AMR][1000 genomes]
rs6036395	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6036396	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6036400	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6036402	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6048764	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6048773	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048783	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048785	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048787	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048789	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048791	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048792	0.94[ASN][1000 genomes]
rs6048793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6076060	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6076069	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083091	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6083109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083117	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083120	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083125	0.94[ASN][1000 genomes]
rs6106650	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6106652	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6114078	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114086	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73303309	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7361799	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8119387	0.95[EUR][1000 genomes];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	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23399800-23402600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr20:23400000-23402600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:23400200-23402400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr20:23400200-23402400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr20:23400200-23402400	Active TSS	HSMMtube	muscle
6	chr20:23400200-23402600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:23400200-23402600	Active TSS	K562	blood
8	chr20:23400400-23402200	Active TSS	Placenta	Placenta
9	chr20:23400400-23402200	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr20:23400400-23402200	Active TSS	GM12878-XiMat	blood
11	chr20:23400400-23402400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr20:23400400-23402400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr20:23400400-23402400	Active TSS	Aorta	Aorta
14	chr20:23400400-23402400	Active TSS	Colon Smooth Muscle	Colon
15	chr20:23400400-23402400	Active TSS	Fetal Muscle Leg	muscle
16	chr20:23400400-23402400	Active TSS	Lung	lung
17	chr20:23400400-23402400	Active TSS	Ovary	ovary
18	chr20:23400400-23402600	Active TSS	Colonic Mucosa	Colon
19	chr20:23400400-23402600	Active TSS	Fetal Muscle Trunk	muscle
20	chr20:23400400-23402600	Active TSS	Left Ventricle	heart
21	chr20:23400400-23402600	Active TSS	Right Atrium	heart
22	chr20:23400400-23402800	Active TSS	Stomach Smooth Muscle	stomach
23	chr20:23400600-23402200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr20:23400600-23402200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:23400600-23402200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr20:23400600-23402200	Active TSS	Duodenum Mucosa	Duodenum
27	chr20:23400600-23402200	Active TSS	Fetal Intestine Small	intestine
28	chr20:23400600-23402200	Active TSS	Fetal Thymus	thymus
29	chr20:23400600-23402200	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr20:23400600-23402200	Active TSS	HMEC	breast
31	chr20:23400600-23402200	Active TSS	Monocytes-CD14+_RO01746	blood
32	chr20:23400600-23402200	Active TSS	NH-A	brain
33	chr20:23400600-23402200	Active TSS	NHDF-Ad	bronchial
34	chr20:23400600-23402400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:23400600-23402400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr20:23400600-23402400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr20:23400600-23402400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr20:23400600-23402400	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr20:23400600-23402400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:23400600-23402400	Active TSS	Muscle Satellite Cultured Cells	--
41	chr20:23400600-23402400	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr20:23400600-23402400	Active TSS	Esophagus	oesophagus
43	chr20:23400600-23402400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr20:23400600-23402400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr20:23400600-23402400	Active TSS	Right Ventricle	heart
46	chr20:23400600-23402400	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr20:23400600-23402400	Active TSS	NHLF	lung
48	chr20:23400600-23402600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr20:23400600-23402600	Active TSS	Psoas Muscle	Psoas
50	chr20:23400600-23402600	Active TSS	HSMM	muscle

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