Variant report

Variant	rs13080059
Chromosome Location	chr3:134029172-134029173
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	CEBPB	chr3:134028934-134029334	A549	lung:	n/a	chr3:134029138-134029151
2	CEBPB	chr3:134028708-134029316	HepG2	liver:	n/a	chr3:134028900-134028913 chr3:134029138-134029151
3	CEBPB	chr3:134028698-134029371	A549	lung:	n/a	chr3:134028900-134028913 chr3:134029138-134029151
4	CEBPB	chr3:134028870-134029267	IMR90	lung:	n/a	chr3:134028900-134028913 chr3:134029138-134029151
5	SP1	chr3:134028767-134029250	A549	lung:	n/a	chr3:134029062-134029076 chr3:134029055-134029069
6	NR2F2	chr3:134028589-134029192	MCF-7	breast:	n/a	n/a
7	STAT3	chr3:134028780-134029367	MCF10A-Er-Src	breast:	n/a	chr3:134028947-134028958
8	RAD21	chr3:134028695-134029292	Hela-S3	cervix:	n/a	n/a
9	FOXA1	chr3:134028646-134029239	HepG2	liver:	n/a	chr3:134028985-134028997
10	CEBPB	chr3:134028732-134029306	Hela-S3	cervix:	n/a	chr3:134028900-134028913 chr3:134029138-134029151
11	EP300	chr3:134028649-134029273	T-47D	breast:	n/a	chr3:134029039-134029053
12	CEBPB	chr3:134028630-134029345	MCF-7	breast:	n/a	chr3:134028900-134028913 chr3:134029138-134029151
13	FOXA1	chr3:134028756-134029187	HepG2	liver:	n/a	chr3:134028985-134028997
14	EP300	chr3:134028716-134029203	HepG2	liver:	n/a	chr3:134029039-134029053
15	TCF12	chr3:134028610-134029282	A549	lung:	n/a	n/a
16	MYBL2	chr3:134028669-134029233	HepG2	liver:	n/a	n/a
17	TEAD4	chr3:134028598-134029252	HepG2	liver:	n/a	n/a
18	CEBPB	chr3:134029063-134029183	HepG2	liver:	n/a	chr3:134029138-134029151
19	STAT1	chr3:134028170-134029211	Hela-S3	cervix:	n/a	chr3:134028947-134028958
20	CEBPB	chr3:134028721-134029301	HepG2	liver:	n/a	chr3:134028900-134028913 chr3:134029138-134029151
21	EP300	chr3:134028829-134029194	Hela-S3	cervix:	n/a	chr3:134029039-134029053
22	HNF4A	chr3:134028714-134029180	HepG2	liver:	n/a	chr3:134028937-134028952
23	HDAC2	chr3:134028640-134029290	HepG2	liver:	n/a	chr3:134029038-134029052
24	GATA3	chr3:134028659-134029226	T-47D	breast:	n/a	n/a
25	FOXA1	chr3:134028676-134029179	T-47D	breast:	n/a	chr3:134028985-134028997
26	FOXA2	chr3:134028661-134029178	HepG2	liver:	n/a	chr3:134028985-134028997
27	STAT3	chr3:134028850-134029197	MCF10A-Er-Src	breast:	n/a	chr3:134028947-134028958
28	CEBPB	chr3:134028679-134029364	MCF-7	breast:	n/a	chr3:134028900-134028913 chr3:134029138-134029151
29	MAZ	chr3:134028886-134029221	Hela-S3	cervix:	n/a	chr3:134029060-134029070
30	ELF1	chr3:134028551-134029244	MCF-7	breast:	n/a	n/a
31	NR2F2	chr3:134028553-134029253	MCF-7	breast:	n/a	n/a
32	FOXA1	chr3:134028660-134029178	HepG2	liver:	n/a	chr3:134028985-134028997
33	EP300	chr3:134028751-134029185	HepG2	liver:	n/a	chr3:134029039-134029053
34	EP300	chr3:134028590-134029215	HepG2	liver:	n/a	chr3:134029039-134029053
35	SP1	chr3:134028651-134029238	HepG2	liver:	n/a	chr3:134029062-134029076 chr3:134029055-134029069
36	STAT3	chr3:134028769-134029211	MCF10A-Er-Src	breast:	n/a	chr3:134028947-134028958
37	SMC3	chr3:134028709-134029251	Hela-S3	cervix:	n/a	n/a
38	FOXA1	chr3:134028670-134029187	T-47D	breast:	n/a	chr3:134028985-134028997
39	MYC	chr3:134028965-134029208	MCF10A-Er-Src	breast:	n/a	chr3:134029060-134029070
40	GATA3	chr3:134028632-134029191	T-47D	breast:	n/a	n/a
41	CEBPB	chr3:134028904-134029314	A549	lung:	n/a	chr3:134029138-134029151
42	MAX	chr3:134028858-134029254	Hela-S3	cervix:	n/a	chr3:134029060-134029070

No.	Distal block	Cell Line	Cell type
1	chr3:134028222..134030305-chr3:134194088..134195794,2	K562	blood:
2	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
3	chr3:134027693..134029568-chr3:134168349..134170249,2	MCF-7	breast:
4	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
5	chr3:134027625..134034860-chr3:134199305..134206618,11	MCF-7	breast:
6	chr3:134027857..134030162-chr3:134031543..134033569,2	K562	blood:
7	chr3:134029018..134030767-chr3:134154072..134156280,2	MCF-7	breast:
8	chr3:134027446..134029898-chr3:134199577..134201556,2	MCF-7	breast:
9	chr3:133929711..133931992-chr3:134027528..134029983,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240006	TF binding region
ENSG00000240006	Chromatin interaction
ENSG00000214289	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000260633	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11917579	1.00[JPT][hapmap]
rs6772494	1.00[JPT][hapmap]
rs9882640	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13080059	FOXL2	cis	parietal	SCAN
rs13080059	TF	cis	parietal	SCAN
rs13080059	CDV3	cis	cerebellum	SCAN
rs13080059	PPP2R3A	cis	cerebellum	SCAN
rs13080059	TMEM22	cis	parietal	SCAN
rs13080059	CCRL1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134023800-134032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134025200-134031600	Weak transcription	Ovary	ovary
3	chr3:134025600-134030800	Weak transcription	Spleen	Spleen
4	chr3:134026000-134029200	Enhancers	HMEC	breast
5	chr3:134026400-134029400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:134026400-134031800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:134026800-134029400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:134026800-134030400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:134026800-134031800	Enhancers	HSMM	muscle
10	chr3:134026800-134032400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:134026800-134034800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:134027000-134030800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:134027000-134031000	Enhancers	Liver	Liver
14	chr3:134027000-134031400	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:134027000-134031600	Enhancers	Colonic Mucosa	Colon
16	chr3:134027000-134031600	Enhancers	Placenta	Placenta
17	chr3:134027000-134032200	Enhancers	Fetal Muscle Leg	muscle
18	chr3:134027000-134032400	Enhancers	HSMMtube	muscle
19	chr3:134027000-134032400	Enhancers	NH-A	brain
20	chr3:134027200-134029400	Enhancers	Stomach Mucosa	stomach
21	chr3:134027200-134030000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:134027400-134029200	Enhancers	Colon Smooth Muscle	Colon
23	chr3:134027400-134029200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr3:134027400-134029400	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr3:134027400-134029400	Enhancers	NHLF	lung
26	chr3:134027400-134029600	Enhancers	Fetal Lung	lung
27	chr3:134027400-134030200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr3:134027400-134031400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:134027400-134031600	Enhancers	Hela-S3	cervix
30	chr3:134027400-134031800	Enhancers	Fetal Intestine Small	intestine
31	chr3:134027400-134032000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:134027400-134032000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:134027400-134032000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:134027400-134032000	Enhancers	Fetal Intestine Large	intestine
35	chr3:134027400-134032200	Enhancers	Osteobl	bone
36	chr3:134027400-134032400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:134027400-134032400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:134027400-134032400	Enhancers	Brain Substantia Nigra	brain
39	chr3:134027400-134032400	Enhancers	NHDF-Ad	bronchial
40	chr3:134027600-134030000	Weak transcription	Esophagus	oesophagus
41	chr3:134027600-134030200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:134027600-134030200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:134027600-134030800	Weak transcription	Right Ventricle	heart
44	chr3:134027600-134031200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:134027600-134031800	Enhancers	Brain Anterior Caudate	brain
46	chr3:134027800-134029200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:134027800-134029200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:134027800-134029800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:134027800-134030000	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:134027800-134030000	Weak transcription	Fetal Heart	heart

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