Variant report

Variant	rs3867429
Chromosome Location	chr5:154092202-154092203
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	MAX	chr5:154091966-154093055	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr5:154092049-154092932	ECC-1	luminal epithelium:	n/a	n/a
3	FOXA1	chr5:154092010-154092510	HepG2	liver:	n/a	n/a
4	MYC	chr5:154092184-154092241	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:154092052-154092520	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr5:154091938-154092551	H1-hESC	embryonic stem cell:	n/a	chr5:154092244-154092253
7	CEBPB	chr5:154092079-154092349	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr5:154091991-154092286	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA3	chr5:154092093-154092651	T-47D	breast:	n/a	n/a
10	POLR2A	chr5:154092089-154092754	MCF-7	breast:	n/a	n/a
11	TAF1	chr5:154092000-154092580	H1-hESC	embryonic stem cell:	n/a	n/a
12	NFIC	chr5:154091980-154092555	ECC-1	luminal epithelium:	n/a	n/a
13	FOXA1	chr5:154092042-154092485	T-47D	breast:	n/a	n/a
14	RXRA	chr5:154092051-154092533	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr5:154091961-154092932	HCT-116	colon:	n/a	n/a
16	JUND	chr5:154092142-154092327	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF12	chr5:154091863-154093165	ECC-1	luminal epithelium:	n/a	chr5:154092244-154092253
18	POLR2A	chr5:154092057-154092598	ECC-1	luminal epithelium:	n/a	n/a
19	SP1	chr5:154091888-154092604	H1-hESC	embryonic stem cell:	n/a	chr5:154092210-154092221 chr5:154092320-154092341
20	MAX	chr5:154092050-154092713	MCF-7	breast:	n/a	n/a
21	TAF1	chr5:154092127-154092557	H1-hESC	embryonic stem cell:	n/a	n/a
22	EP300	chr5:154091945-154093131	ECC-1	luminal epithelium:	n/a	n/a
23	FOXA1	chr5:154092089-154092405	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr5:154092099-154092767	MCF-7	breast:	n/a	n/a
25	MYC	chr5:154092150-154092382	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr5:154092007-154092628	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr5:154091749-154092842	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr5:154091974-154092938	MCF-7	breast:	n/a	n/a
29	USF2	chr5:154092158-154092540	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZNF143	chr5:154091962-154092989	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOXA1	chr5:154092022-154092389	ECC-1	luminal epithelium:	n/a	n/a
32	TCF12	chr5:154092044-154092507	H1-hESC	embryonic stem cell:	n/a	chr5:154092244-154092253
33	TCF12	chr5:154091854-154093130	ECC-1	luminal epithelium:	n/a	chr5:154092244-154092253
34	JUND	chr5:154092038-154092520	H1-hESC	embryonic stem cell:	n/a	chr5:154092323-154092332
35	EP300	chr5:154091992-154092486	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr5:154092200-154092350	NHEK	skin:	n/a	n/a
37	FOXA1	chr5:154092104-154092517	T-47D	breast:	n/a	n/a
38	RAD21	chr5:154092012-154092428	H1-hESC	embryonic stem cell:	n/a	chr5:154092403-154092417 chr5:154092410-154092420
39	YY1	chr5:154092013-154092392	HCT-116	colon:	n/a	n/a
40	POLR2A	chr5:154091983-154092647	HCT-116	colon:	n/a	n/a
41	MAFK	chr5:154092059-154092307	H1-hESC	embryonic stem cell:	n/a	n/a
42	NR2F2	chr5:154091857-154093733	MCF-7	breast:	n/a	n/a
43	RAD21	chr5:154091945-154092622	H1-hESC	embryonic stem cell:	n/a	chr5:154092403-154092417 chr5:154092410-154092420
44	POLR2A	chr5:154092051-154092548	H1-hESC	embryonic stem cell:	n/a	n/a
45	CHD2	chr5:154092053-154092526	H1-hESC	embryonic stem cell:	n/a	n/a
46	RFX5	chr5:154092196-154092545	H1-hESC	embryonic stem cell:	n/a	chr5:154092322-154092331 chr5:154092378-154092387 chr5:154092376-154092390 chr5:154092373-154092389
47	TBP	chr5:154091993-154092579	H1-hESC	embryonic stem cell:	n/a	n/a
48	FOXA2	chr5:154092071-154092335	HepG2	liver:	n/a	n/a
49	BACH1	chr5:154092009-154092357	H1-hESC	embryonic stem cell:	n/a	n/a
50	MYC	chr5:154092154-154092330	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:154082225..154089110-chr5:154090425..154094066,7	MCF-7	breast:
2	chr5:154091014..154094062-chr5:154133007..154138054,7	MCF-7	breast:
3	chr5:154090008..154095548-chr5:154132332..154137735,10	MCF-7	breast:

Variant related genes	Relation type
LARP1	TF binding region
ENSG00000155506	Chromatin interaction
ENSG00000263478	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11740589	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs3853757	1.00[ASN][1000 genomes]
rs55849543	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863954	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797583	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276703	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7328	1.00[CHD][hapmap]
rs7710726	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734591	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3867429	LARP1	cis	Whole Blood	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154071400-154093400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:154072200-154092600	Weak transcription	Adipose Nuclei	Adipose
3	chr5:154074200-154108600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:154074200-154120000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:154087800-154092600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:154088600-154098200	Weak transcription	Right Atrium	heart
7	chr5:154088800-154092600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:154089000-154092400	Weak transcription	HMEC	breast
9	chr5:154089000-154092600	Weak transcription	NHDF-Ad	bronchial
10	chr5:154089000-154093400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:154089200-154092600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:154089600-154092600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:154089600-154093000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:154089600-154093200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:154090000-154092400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:154090000-154093200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:154091600-154093200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr5:154091600-154093600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:154091800-154092400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:154091800-154092400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:154091800-154092400	Enhancers	Colonic Mucosa	Colon
22	chr5:154091800-154092400	Enhancers	Esophagus	oesophagus
23	chr5:154091800-154092400	Enhancers	Hela-S3	cervix
24	chr5:154091800-154092800	Enhancers	Lung	lung
25	chr5:154091800-154093000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr5:154091800-154093000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr5:154091800-154093400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:154091800-154093600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr5:154091800-154093600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr5:154091800-154094000	Enhancers	Liver	Liver
31	chr5:154091800-154094200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:154091800-154094400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:154091800-154094400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr5:154092000-154092400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:154092000-154092400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:154092000-154092400	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr5:154092000-154092400	Enhancers	Placenta	Placenta
38	chr5:154092000-154092600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:154092000-154092600	Flanking Active TSS	Fetal Intestine Large	intestine
40	chr5:154092000-154092600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr5:154092000-154092800	Enhancers	Right Ventricle	heart
42	chr5:154092000-154092800	Flanking Active TSS	NHEK	skin
43	chr5:154092000-154093000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:154092000-154093400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr5:154092000-154093600	Enhancers	Spleen	Spleen
46	chr5:154092000-154094200	Flanking Active TSS	HepG2	liver
47	chr5:154092000-154094400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:154092000-154094400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:154092000-154094400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:154092000-154094400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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