Variant report

Variant	rs6079178
Chromosome Location	chr20:13781531-13781532
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:13781349-13781753	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr20:13781480-13781630	HCPEpiC	choroid plexus:	n/a	n/a
3	HDAC2	chr20:13781249-13781783	HepG2	liver:	n/a	n/a
4	MAX	chr20:13781252-13781821	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:13781322-13781737	HUVEC	blood vessel:	n/a	n/a
6	GATA3	chr20:13781322-13781864	T-47D	breast:	n/a	n/a
7	TBP	chr20:13781418-13781670	HepG2	liver:	n/a	n/a
8	MYC	chr20:13781531-13781664	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:13781455-13781627	MCF-7	breast:	n/a	n/a
10	TCF12	chr20:13781030-13781978	SK-N-SH	brain:	n/a	n/a
11	MAX	chr20:13781402-13781818	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr20:13781404-13781679	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr20:13781307-13781621	SK-N-SH	brain:	n/a	n/a
14	REST	chr20:13781294-13781836	MCF-7	breast:	n/a	n/a
15	MYC	chr20:13781491-13781680	MCF-7	breast:	n/a	n/a
16	MYC	chr20:13781163-13781991	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr20:13781365-13781821	MCF-7	breast:	n/a	n/a
18	PBX3	chr20:13781195-13781865	SK-N-SH	brain:	n/a	n/a
19	STAT3	chr20:13781424-13781728	MCF10A-Er-Src	breast:	n/a	n/a
20	MAX	chr20:13781390-13781801	HepG2	liver:	n/a	n/a
21	TEAD4	chr20:13781121-13781888	HepG2	liver:	n/a	n/a
22	MAFK	chr20:13781381-13781704	HepG2	liver:	n/a	n/a
23	MAX	chr20:13781247-13781893	HepG2	liver:	n/a	n/a
24	EP300	chr20:13781295-13781790	SK-N-SH_RA	brain:	n/a	n/a
25	MXI1	chr20:13781297-13781961	IMR90	lung:	n/a	n/a
26	EP300	chr20:13781246-13781800	HepG2	liver:	n/a	n/a
27	SIN3AK20	chr20:13781343-13781858	MCF-7	breast:	n/a	n/a
28	MYC	chr20:13781284-13781874	MCF10A-Er-Src	breast:	n/a	n/a
29	RFX5	chr20:13781459-13781578	HepG2	liver:	n/a	n/a
30	POLR2A	chr20:13781227-13781807	SK-N-SH	brain:	n/a	n/a
31	MXI1	chr20:13781066-13781940	SK-N-SH	brain:	n/a	n/a
32	FOS	chr20:13781337-13781752	MCF10A-Er-Src	breast:	n/a	n/a
33	GATA3	chr20:13781255-13781934	MCF-7	breast:	n/a	n/a
34	EP300	chr20:13781150-13781854	SK-N-SH	brain:	n/a	chr20:13781820-13781834
35	EP300	chr20:13781346-13781808	T-47D	breast:	n/a	n/a
36	MYC	chr20:13781483-13781714	MCF-7	breast:	n/a	n/a
37	NFIC	chr20:13781235-13781836	SK-N-SH	brain:	n/a	n/a
38	NFIC	chr20:13781232-13781821	HepG2	liver:	n/a	n/a
39	MAX	chr20:13781309-13781874	SK-N-SH	brain:	n/a	n/a
40	SIN3AK20	chr20:13781264-13781776	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr20:13781459-13781633	A549	lung:	n/a	n/a
42	STAT3	chr20:13780854-13781863	MCF10A-Er-Src	breast:	n/a	chr20:13780865-13780879
43	EP300	chr20:13781441-13781719	HepG2	liver:	n/a	n/a
44	EP300	chr20:13781299-13781804	SK-N-SH_RA	brain:	n/a	n/a
45	STAT3	chr20:13781433-13781724	MCF10A-Er-Src	breast:	n/a	n/a
46	RCOR1	chr20:13781049-13781833	IMR90	lung:	n/a	n/a
47	HNF4A	chr20:13781303-13781725	HepG2	liver:	n/a	chr20:13781518-13781533
48	GATA3	chr20:13781106-13781979	SK-N-SH	brain:	n/a	n/a
49	REST	chr20:13781388-13781783	MCF-7	breast:	n/a	n/a
50	CEBPB	chr20:13781258-13781711	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13764939..13767179-chr20:13781329..13782936,2	MCF-7	breast:
2	chr20:13771650..13774538-chr20:13781308..13785639,3	K562	blood:

No data

Variant related genes	Relation type
NDUFAF5	TF binding region
ENSG00000089048	Chromatin interaction
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13039364	0.81[AFR][1000 genomes]
rs13042637	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1547920	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17812441	0.81[AFR][1000 genomes]
rs1999112	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2031933	0.83[ASN][1000 genomes]
rs2209993	0.90[ASN][1000 genomes]
rs2209994	0.90[ASN][1000 genomes]
rs2327797	0.81[AFR][1000 genomes]
rs2423745	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2423749	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2423750	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2423753	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3180370	0.96[ASN][1000 genomes]
rs34195844	0.81[AFR][1000 genomes]
rs34449907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34806363	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35361761	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35632254	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4813142	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814256	0.85[ASN][1000 genomes]
rs4814258	0.83[ASN][1000 genomes]
rs55814427	0.81[AFR][1000 genomes]
rs56043440	0.81[AFR][1000 genomes]
rs6033816	0.83[ASN][1000 genomes]
rs6033819	0.90[ASN][1000 genomes]
rs6033821	0.98[ASN][1000 genomes]
rs6042351	0.89[ASN][1000 genomes]
rs6042357	0.82[ASN][1000 genomes]
rs6042362	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6074643	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074644	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079156	0.81[AFR][1000 genomes]
rs6079158	0.81[AFR][1000 genomes]
rs6079162	0.86[ASN][1000 genomes]
rs6079165	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079166	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6079176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079182	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110026	0.86[ASN][1000 genomes]
rs6110035	0.90[ASN][1000 genomes]
rs6134968	0.89[ASN][1000 genomes]
rs62209178	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62209207	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68012295	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754796	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr20:13766400-13793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:13766400-13796800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:13767400-13792600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:13767600-13789800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr20:13767600-13799600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:13767800-13799400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr20:13767800-13800600	Weak transcription	Stomach Mucosa	stomach
8	chr20:13768000-13786000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr20:13768000-13794800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr20:13768000-13799800	Strong transcription	Fetal Thymus	thymus
11	chr20:13768200-13799800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:13768200-13799800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr20:13768400-13799600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr20:13768600-13799600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr20:13768800-13786200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr20:13768800-13799600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr20:13769000-13799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr20:13769200-13789800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr20:13769200-13799600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr20:13769400-13786000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr20:13769400-13799400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr20:13769400-13802000	Strong transcription	A549	lung
23	chr20:13769600-13799400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr20:13769800-13785600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr20:13769800-13785800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr20:13769800-13786400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr20:13769800-13786400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr20:13769800-13787200	Strong transcription	Fetal Intestine Large	intestine
29	chr20:13769800-13788600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr20:13770000-13787000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr20:13770200-13799600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr20:13770400-13785600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr20:13770600-13784200	Strong transcription	GM12878-XiMat	blood
34	chr20:13770600-13799400	Strong transcription	Primary T cells from cord blood	blood
35	chr20:13771000-13784000	Strong transcription	Primary B cells from cord blood	blood
36	chr20:13772600-13789000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr20:13773600-13799400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:13776000-13782200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr20:13777000-13788000	Weak transcription	Hela-S3	cervix
40	chr20:13777200-13782200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr20:13777200-13782600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr20:13777400-13782200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr20:13778000-13782800	Weak transcription	Aorta	Aorta
44	chr20:13778000-13784600	Weak transcription	Small Intestine	intestine
45	chr20:13778000-13789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr20:13778200-13782000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr20:13778200-13783600	Weak transcription	Right Ventricle	heart
48	chr20:13778400-13782200	Weak transcription	Psoas Muscle	Psoas
49	chr20:13778800-13784000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr20:13779200-13782400	Genic enhancers	Adipose Nuclei	Adipose

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