Variant report

Variant	rs2459240
Chromosome Location	chr1:165508685-165508686
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	FOS	chr1:165508580-165508931	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:165508571-165508931	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr1:165508598-165508903	HepG2	liver:	n/a	n/a
4	JUND	chr1:165508609-165508912	Hela-S3	cervix:	n/a	chr1:165508745-165508756
5	STAT3	chr1:165508621-165508915	MCF10A-Er-Src	breast:	n/a	n/a
6	FOSL2	chr1:165508552-165508988	A549	lung:	n/a	chr1:165508746-165508757
7	RFX5	chr1:165508644-165508873	Hela-S3	cervix:	n/a	n/a
8	FOXA1	chr1:165508591-165509006	HepG2	liver:	n/a	n/a
9	CEBPB	chr1:165508591-165508932	Hela-S3	cervix:	n/a	n/a
10	NR2F2	chr1:165508495-165508906	MCF-7	breast:	n/a	n/a
11	FOXA1	chr1:165508533-165508886	HepG2	liver:	n/a	n/a
12	E2F4	chr1:165508660-165509026	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:165508582-165508940	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:165508593-165508925	MCF10A-Er-Src	breast:	n/a	n/a
15	FOSL2	chr1:165508597-165508877	HepG2	liver:	n/a	chr1:165508746-165508757
16	ARID3A	chr1:165508617-165508909	HepG2	liver:	n/a	n/a
17	USF2	chr1:165508532-165508849	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr1:165508474-165509047	MCF-7	breast:	n/a	n/a
19	JUND	chr1:165508659-165508858	H1-hESC	embryonic stem cell:	n/a	chr1:165508745-165508756
20	FOSL2	chr1:165508470-165508977	MCF-7	breast:	n/a	chr1:165508746-165508757
21	FOSL2	chr1:165508575-165508855	HepG2	liver:	n/a	chr1:165508746-165508757
22	JUND	chr1:165508579-165508863	HepG2	liver:	n/a	chr1:165508745-165508756

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RXRG-1	chr1:165508672-165508849	ENSG00000237463.1

Variant related genes	Relation type
LRRC52	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10494443	0.85[EUR][1000 genomes]
rs10494445	1.00[CEU][hapmap]
rs1326375	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1648111	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs166949	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846405	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16846410	0.85[EUR][1000 genomes]
rs16846549	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16846612	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16846621	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16847312	1.00[CEU][hapmap]
rs184038	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs184039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs191746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs192586	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs192587	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433131	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2485399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2485400	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2485401	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2485408	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs285423	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs285424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs285433	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285434	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285436	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285437	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285440	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285441	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285442	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs285444	1.00[CEU][hapmap]
rs285445	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285446	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs285447	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs285449	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs285450	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs285451	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs285452	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285453	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs285454	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs366124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs369231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs375780	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs385649	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs386186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs390395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs404612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs415710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs421361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs424313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58628453	0.85[EUR][1000 genomes]
rs6426916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6659141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6666562	1.00[CEU][hapmap]
rs71485870	0.93[AFR][1000 genomes]
rs74118810	0.81[AMR][1000 genomes]
rs74120723	0.85[EUR][1000 genomes]
rs74120729	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs796570	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165502600-165508800	Weak transcription	Right Ventricle	heart
2	chr1:165503600-165509000	Weak transcription	Psoas Muscle	Psoas
3	chr1:165503600-165509000	Weak transcription	Right Atrium	heart
4	chr1:165505600-165513000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:165507200-165510400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:165507600-165509600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:165507600-165512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:165508400-165509000	Enhancers	A549	lung
9	chr1:165508400-165509400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:165508400-165510800	Enhancers	Fetal Muscle Leg	muscle
11	chr1:165508400-165510800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:165508600-165508800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr1:165508600-165509000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:165508600-165509800	Enhancers	Aorta	Aorta
15	chr1:165508600-165509800	Enhancers	Fetal Muscle Trunk	muscle
16	chr1:165508600-165510400	Enhancers	Placenta	Placenta
17	chr1:165508600-165510600	Enhancers	Left Ventricle	heart

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