Variant report

Variant	rs6048959
Chromosome Location	chr20:23616305-23616306
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	STAT3	chr20:23616160-23616494	MCF10A-Er-Src	breast:	n/a	chr20:23616286-23616297
2	FOS	chr20:23616267-23616627	MCF10A-Er-Src	breast:	n/a	chr20:23616508-23616517
3	NR3C1	chr20:23615744-23616307	A549	lung:	n/a	chr20:23616031-23616045 chr20:23616030-23616046 chr20:23616027-23616048 chr20:23616031-23616045 chr20:23616030-23616047 chr20:23616030-23616046
4	POLR2A	chr20:23615415-23616432	HepG2	liver:	n/a	n/a
5	CEBPB	chr20:23616224-23616387	A549	lung:	n/a	chr20:23616308-23616319
6	POLR2A	chr20:23614494-23618787	HepG2	liver:	n/a	n/a
7	MYC	chr20:23615927-23616634	MCF10A-Er-Src	breast:	n/a	chr20:23616459-23616470 chr20:23616461-23616468 chr20:23616459-23616470 chr20:23616460-23616469 chr20:23616308-23616317
8	POLR2A	chr20:23611829-23619325	HepG2	liver:	n/a	n/a
9	HEY1	chr20:23615419-23616671	HepG2	liver:	n/a	n/a
10	POLR2A	chr20:23615259-23617766	HepG2	liver:	n/a	n/a
11	CEBPB	chr20:23616136-23616481	HepG2	liver:	n/a	chr20:23616308-23616319
12	POLR2A	chr20:23616224-23616343	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr20:23616233-23616647	MCF10A-Er-Src	breast:	n/a	chr20:23616508-23616517
14	FOS	chr20:23616120-23616650	MCF10A-Er-Src	breast:	n/a	chr20:23616508-23616517
15	FOS	chr20:23616269-23616596	MCF10A-Er-Src	breast:	n/a	chr20:23616508-23616517
16	HEY1	chr20:23615393-23617806	HepG2	liver:	n/a	n/a
17	STAT3	chr20:23616030-23616487	MCF10A-Er-Src	breast:	n/a	chr20:23616286-23616297
18	POLR2A	chr20:23614496-23617566	HepG2	liver:	n/a	n/a
19	POLR2A	chr20:23611753-23618814	HepG2	liver:	n/a	n/a
20	STAT3	chr20:23616114-23616575	MCF10A-Er-Src	breast:	n/a	chr20:23616286-23616297
21	TEAD4	chr20:23615998-23616595	HepG2	liver:	n/a	n/a
22	POLR2A	chr20:23615326-23618779	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr20:23615277-23616335	K562	blood:	n/a	n/a
24	POLR2A	chr20:23615551-23616337	HepG2	liver:	n/a	n/a
25	STAT3	chr20:23616160-23616491	MCF10A-Er-Src	breast:	n/a	chr20:23616286-23616297
26	MYC	chr20:23616040-23616426	MCF10A-Er-Src	breast:	n/a	chr20:23616308-23616317
27	STAT3	chr20:23616135-23616493	MCF10A-Er-Src	breast:	n/a	chr20:23616286-23616297
28	MBD4	chr20:23615477-23616458	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23604645..23607070-chr20:23613987..23616956,2	K562	blood:
2	chr20:23400310..23402508-chr20:23615661..23618868,3	MCF-7	breast:
3	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
4	chr20:23615491..23618366-chr20:23625789..23627708,2	MCF-7	breast:
5	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:
6	chr20:23615462..23617688-chr20:23624542..23627030,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270001	TF binding region
ENSG00000125812	Chromatin interaction
ENSG00000270001	Chromatin interaction
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16985393	1.00[GIH][hapmap]
rs1966182	1.00[GIH][hapmap]
rs2405390	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs2405391	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6048913	1.00[CEU][hapmap]
rs6048962	1.00[AMR][1000 genomes]
rs6106686	1.00[CEU][hapmap]
rs6114194	1.00[CEU][hapmap]
rs6515370	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv964381	chr20:23614805-23621846	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:23606600-23617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:23606800-23616600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:23609800-23616800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr20:23610200-23616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr20:23610200-23617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr20:23610200-23617000	Weak transcription	K562	blood
11	chr20:23610400-23616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr20:23610400-23616800	Weak transcription	NH-A	brain
13	chr20:23610400-23618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr20:23610600-23616800	Weak transcription	Hela-S3	cervix
15	chr20:23610800-23616800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr20:23610800-23617400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr20:23612000-23617000	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr20:23612600-23616600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr20:23612600-23616600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr20:23612600-23617200	Genic enhancers	Fetal Muscle Leg	muscle
21	chr20:23612800-23617200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr20:23613000-23616800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr20:23613800-23617200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr20:23614200-23616600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr20:23614400-23616600	Enhancers	Psoas Muscle	Psoas
26	chr20:23614600-23616600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr20:23614600-23617200	Genic enhancers	Gastric	stomach
28	chr20:23614600-23617400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr20:23614800-23616600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr20:23614800-23617200	Genic enhancers	Lung	lung
31	chr20:23614800-23617200	Genic enhancers	Spleen	Spleen
32	chr20:23614800-23617400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr20:23614800-23617400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr20:23615000-23616400	Genic enhancers	Pancreas	Pancrea
35	chr20:23615000-23616600	Enhancers	Right Atrium	heart
36	chr20:23615000-23616600	Enhancers	HSMMtube	muscle
37	chr20:23615000-23616800	Weak transcription	Thymus	Thymus
38	chr20:23615000-23616800	Weak transcription	A549	lung
39	chr20:23615000-23617000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
40	chr20:23615000-23618000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
41	chr20:23615200-23616400	Genic enhancers	Brain Cingulate Gyrus	brain
42	chr20:23615200-23616400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
43	chr20:23615200-23617000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:23615200-23617000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr20:23615200-23617000	Transcr. at gene 5' and 3'	HepG2	liver
46	chr20:23615400-23616400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
47	chr20:23615400-23616600	Genic enhancers	NHEK	skin
48	chr20:23615400-23616600	Genic enhancers	NHLF	lung
49	chr20:23615400-23616800	Enhancers	Brain Germinal Matrix	brain
50	chr20:23615400-23617200	Enhancers	Placenta	Placenta

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