Variant report

Variant	rs6042362
Chromosome Location	chr20:13769127-13769128
allele	A/G
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	CTCF	chr20:13768925-13769134	NHEK	skin:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
2	MAFK	chr20:13768958-13769172	HepG2	liver:	n/a	n/a
3	FOS	chr20:13768946-13769302	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr20:13768906-13769141	K562	blood:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
5	CTCF	chr20:13768914-13769136	LNCaP	prostate:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
6	CTCF	chr20:13768814-13769194	HCT-116	colon:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
7	CTCF	chr20:13768980-13769130	GM12875	blood:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
8	JUN	chr20:13769068-13769486	HepG2	liver:	n/a	n/a
9	CTCF	chr20:13768684-13769301	HCT-116	colon:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
10	E2F4	chr20:13768956-13769431	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr20:13768980-13769130	HEK293	kidney:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
12	WRNIP1	chr20:13768944-13769144	GM12878	blood:	n/a	n/a
13	CTCF	chr20:13768854-13769251	HepG2	liver:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
14	RAD21	chr20:13768825-13769250	HepG2	liver:	n/a	chr20:13769001-13769014 chr20:13769007-13769016 chr20:13768998-13769017
15	CTCF	chr20:13769020-13769170	A549	lung:	n/a	n/a
16	CTCF	chr20:13768905-13769140	GM10266	blood:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
17	CTCF	chr20:13768919-13769153	MCF-7	breast:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
18	CTCF	chr20:13768980-13769130	HVMF	connective:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
19	CTCF	chr20:13768929-13769131	HepG2	liver:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
20	CTCF	chr20:13768930-13769143	Hela-S3	cervix:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
21	ZNF143	chr20:13768846-13769197	GM12878	blood:	n/a	n/a
22	CTCF	chr20:13768915-13769136	K562	blood:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
23	FOS	chr20:13768920-13769410	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr20:13768885-13769161	Medullo	brain:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
25	CTCF	chr20:13768904-13769157	MCF-7	breast:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
26	CTCF	chr20:13768812-13769205	IMR90	lung:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
27	RAD21	chr20:13768878-13769129	SK-N-SH_RA	brain:	n/a	chr20:13769001-13769014 chr20:13769007-13769016 chr20:13768998-13769017
28	CTCF	chr20:13769020-13769170	RPTEC	kidney:	n/a	n/a
29	CEBPB	chr20:13769121-13769448	IMR90	lung:	n/a	chr20:13769377-13769390 chr20:13769276-13769287
30	CTCF	chr20:13768670-13769212	K562	blood:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
31	CTCF	chr20:13768980-13769130	NHEK	skin:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
32	RAD21	chr20:13768793-13769287	A549	lung:	n/a	chr20:13769001-13769014 chr20:13769007-13769016 chr20:13768998-13769017
33	FOS	chr20:13768954-13769298	MCF10A-Er-Src	breast:	n/a	n/a
34	CEBPB	chr20:13768939-13769403	H1-hESC	embryonic stem cell:	n/a	chr20:13769377-13769390 chr20:13769276-13769287
35	GTF2F1	chr20:13768932-13769127	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr20:13768896-13769131	H1-hESC	embryonic stem cell:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
37	CTCF	chr20:13768935-13769135	GM19238	blood:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
38	CTCF	chr20:13769000-13769150	HEK293	kidney:	n/a	chr20:13769002-13769015 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
39	CTCF	chr20:13769000-13769150	WI-38	lung:	n/a	chr20:13769002-13769015 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
40	MYC	chr20:13768886-13769393	MCF10A-Er-Src	breast:	n/a	chr20:13769118-13769127
41	RAD21	chr20:13768702-13769342	SK-N-SH	brain:	n/a	chr20:13769001-13769014 chr20:13769007-13769016 chr20:13768998-13769017
42	STAT3	chr20:13768964-13769407	MCF10A-Er-Src	breast:	n/a	chr20:13769145-13769168
43	RAD21	chr20:13768852-13769174	Hela-S3	cervix:	n/a	chr20:13769001-13769014 chr20:13769007-13769016 chr20:13768998-13769017
44	RFX5	chr20:13768960-13769193	HepG2	liver:	n/a	n/a
45	SMC3	chr20:13768842-13769434	HepG2	liver:	n/a	chr20:13769002-13769016
46	CTCF	chr20:13769020-13769170	HAc	cerebellar:	n/a	n/a
47	RAD21	chr20:13768867-13769139	HepG2	liver:	n/a	chr20:13769001-13769014 chr20:13769007-13769016 chr20:13768998-13769017
48	CTCF	chr20:13768869-13769155	A549	lung:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
49	POLR2A	chr20:13768813-13769154	MCF10A-Er-Src	breast:	n/a	n/a
50	MAX	chr20:13768980-13769134	HepG2	liver:	n/a	chr20:13769118-13769127

No.	Distal block	Cell Line	Cell type
1	chr20:13768422..13770202-chr20:13776698..13778649,2	K562	blood:
2	chr20:13769039..13770895-chr20:13773639..13775418,2	K562	blood:
3	chr20:13769074..13771240-chr20:13798879..13801315,2	K562	blood:
4	chr20:13767767..13769500-chr20:13771706..13774307,2	MCF-7	breast:

Variant related genes	Relation type
NDUFAF5	TF binding region
ESF1	TF binding region
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13042637	0.88[ASN][1000 genomes]
rs1547920	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1999112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031933	0.90[ASN][1000 genomes]
rs2209993	0.97[ASN][1000 genomes]
rs2209994	0.97[ASN][1000 genomes]
rs2423745	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2423749	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423750	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423753	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3180370	0.90[ASN][1000 genomes]
rs34449907	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34806363	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35361761	0.81[ASN][1000 genomes]
rs35632254	0.81[ASN][1000 genomes]
rs4813142	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4814258	0.90[ASN][1000 genomes]
rs6033816	0.90[ASN][1000 genomes]
rs6033819	0.97[ASN][1000 genomes]
rs6033821	0.91[ASN][1000 genomes]
rs6042351	0.83[ASN][1000 genomes]
rs6042357	0.89[ASN][1000 genomes]
rs6074643	0.90[ASN][1000 genomes]
rs6074644	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6079165	0.84[ASN][1000 genomes]
rs6079166	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6079176	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079178	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079181	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6079182	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6105162	0.85[ASN][1000 genomes]
rs6110035	0.97[ASN][1000 genomes]
rs6134968	0.83[ASN][1000 genomes]
rs62209178	0.84[ASN][1000 genomes]
rs62209207	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68012295	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs754796	0.90[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	chr20:13766400-13769400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr20:13766400-13769800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:13766400-13770000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:13766400-13793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr20:13766400-13796800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:13766600-13772200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr20:13766800-13769200	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr20:13766800-13770400	Weak transcription	Lung	lung
9	chr20:13766800-13781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr20:13767000-13769400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr20:13767000-13770600	Weak transcription	Colonic Mucosa	Colon
12	chr20:13767200-13769400	Enhancers	Primary T cells from cord blood	blood
13	chr20:13767200-13769800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr20:13767200-13769800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:13767200-13769800	Weak transcription	Spleen	Spleen
16	chr20:13767200-13770200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr20:13767200-13770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr20:13767200-13771000	Weak transcription	Primary B cells from cord blood	blood
19	chr20:13767200-13771400	Weak transcription	Fetal Kidney	kidney
20	chr20:13767400-13769200	Enhancers	Fetal Intestine Small	intestine
21	chr20:13767400-13769600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:13767400-13769800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr20:13767400-13769800	Weak transcription	Fetal Intestine Large	intestine
24	chr20:13767400-13769800	Weak transcription	Gastric	stomach
25	chr20:13767400-13770000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr20:13767400-13770000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr20:13767400-13770000	Enhancers	Liver	Liver
28	chr20:13767400-13770000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr20:13767400-13770400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr20:13767400-13770400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr20:13767400-13770800	Weak transcription	Ovary	ovary
32	chr20:13767400-13771000	Weak transcription	Aorta	Aorta
33	chr20:13767400-13771400	Weak transcription	Right Ventricle	heart
34	chr20:13767400-13771800	Weak transcription	Pancreas	Pancrea
35	chr20:13767400-13772400	Weak transcription	Esophagus	oesophagus
36	chr20:13767400-13792600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr20:13767600-13769200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr20:13767600-13769400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr20:13767600-13769400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:13767600-13769400	Genic enhancers	A549	lung
41	chr20:13767600-13769400	Weak transcription	Osteobl	bone
42	chr20:13767600-13769600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:13767600-13769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr20:13767600-13769800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr20:13767600-13769800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr20:13767600-13769800	Weak transcription	HSMM	muscle
47	chr20:13767600-13770000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr20:13767600-13770000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr20:13767600-13770000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr20:13767600-13770400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links