Variant report

Variant	rs6079175
Chromosome Location	chr20:13768685-13768686
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	chr20:13768600-13768750	GM12878	blood:	n/a	n/a
2	CTCF	chr20:13768684-13769301	HCT-116	colon:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
3	CTCF	chr20:13768620-13768770	GM12872	blood:	n/a	n/a
4	CTCF	chr20:13768640-13768790	HepG2	liver:	n/a	n/a
5	CTCF	chr20:13768670-13769212	K562	blood:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
6	CTCF	chr20:13768600-13768750	GM12872	blood:	n/a	n/a
7	CTCF	chr20:13768507-13769585	A549	lung:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
8	CTCF	chr20:13768620-13768770	GM12878	blood:	n/a	n/a
9	NFIC	chr20:13768601-13769530	HepG2	liver:	n/a	n/a
10	CTCF	chr20:13768600-13768750	GM12873	blood:	n/a	n/a
11	CTCF	chr20:13768526-13769299	SK-N-SH	brain:	n/a	chr20:13769002-13769015 chr20:13768995-13769016 chr20:13769000-13769018 chr20:13769003-13769013 chr20:13769006-13769015
12	CTCF	chr20:13768600-13768750	HUVEC	blood vessel:	n/a	n/a
13	CTCF	chr20:13768600-13768750	HPF	lung:	n/a	n/a
14	CTCF	chr20:13768600-13768750	Caco-2	colon:	n/a	n/a
15	CTCF	chr20:13768640-13768790	Caco-2	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13768422..13770202-chr20:13776698..13778649,2	K562	blood:
2	chr20:13767767..13769500-chr20:13771706..13774307,2	MCF-7	breast:

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

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2094652	0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2327796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2423754	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs243917	1.00[EUR][1000 genomes]
rs34901599	1.00[AMR][1000 genomes]
rs4239710	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814255	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814257	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4814259	0.88[AFR][1000 genomes]
rs6033822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042334	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042344	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6074639	0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	chr20:13766800-13769000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:13766800-13769200	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr20:13766800-13770400	Weak transcription	Lung	lung
10	chr20:13766800-13781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr20:13767000-13769400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr20:13767000-13770600	Weak transcription	Colonic Mucosa	Colon
13	chr20:13767200-13768800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr20:13767200-13768800	Enhancers	Thymus	Thymus
15	chr20:13767200-13769400	Enhancers	Primary T cells from cord blood	blood
16	chr20:13767200-13769800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr20:13767200-13769800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:13767200-13769800	Weak transcription	Spleen	Spleen
19	chr20:13767200-13770200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr20:13767200-13770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr20:13767200-13771000	Weak transcription	Primary B cells from cord blood	blood
22	chr20:13767200-13771400	Weak transcription	Fetal Kidney	kidney
23	chr20:13767400-13769000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr20:13767400-13769200	Enhancers	Fetal Intestine Small	intestine
25	chr20:13767400-13769600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr20:13767400-13769800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr20:13767400-13769800	Weak transcription	Fetal Intestine Large	intestine
28	chr20:13767400-13769800	Weak transcription	Gastric	stomach
29	chr20:13767400-13770000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr20:13767400-13770000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr20:13767400-13770000	Enhancers	Liver	Liver
32	chr20:13767400-13770000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr20:13767400-13770400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr20:13767400-13770400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr20:13767400-13770800	Weak transcription	Ovary	ovary
36	chr20:13767400-13771000	Weak transcription	Aorta	Aorta
37	chr20:13767400-13771400	Weak transcription	Right Ventricle	heart
38	chr20:13767400-13771800	Weak transcription	Pancreas	Pancrea
39	chr20:13767400-13772400	Weak transcription	Esophagus	oesophagus
40	chr20:13767400-13792600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr20:13767600-13768800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr20:13767600-13768800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr20:13767600-13769200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr20:13767600-13769400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr20:13767600-13769400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr20:13767600-13769400	Genic enhancers	A549	lung
47	chr20:13767600-13769400	Weak transcription	Osteobl	bone
48	chr20:13767600-13769600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr20:13767600-13769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr20:13767600-13769800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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