Variant report

Variant	rs550255
Chromosome Location	chr11:94135783-94135784
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	ESR1	chr11:94135511-94135848	T-47D	breast:	n/a	chr11:94135697-94135714
2	EP300	chr11:94135454-94135873	HepG2	liver:	n/a	n/a
3	FOXA1	chr11:94135508-94135920	HepG2	liver:	n/a	n/a
4	FOS	chr11:94135607-94135832	MCF10A-Er-Src	breast:	n/a	chr11:94135747-94135754 chr11:94135747-94135755
5	FOXA1	chr11:94135470-94135863	HepG2	liver:	n/a	n/a
6	ESR1	chr11:94135552-94135823	ECC-1	luminal epithelium:	n/a	chr11:94135697-94135714
7	FOS	chr11:94135633-94135840	MCF10A-Er-Src	breast:	n/a	chr11:94135747-94135754 chr11:94135747-94135755
8	FOSL2	chr11:94135486-94135934	HepG2	liver:	n/a	chr11:94135747-94135754 chr11:94135869-94135880 chr11:94135747-94135755
9	FOXA2	chr11:94135551-94135807	HepG2	liver:	n/a	n/a
10	STAT3	chr11:94135606-94135787	MCF10A-Er-Src	breast:	n/a	n/a
11	FOXA1	chr11:94135559-94135840	HepG2	liver:	n/a	n/a
12	FOS	chr11:94135675-94135849	MCF10A-Er-Src	breast:	n/a	chr11:94135747-94135754 chr11:94135747-94135755
13	MAX	chr11:94135734-94135801	HepG2	liver:	n/a	n/a
14	FOXA1	chr11:94135417-94135894	HepG2	liver:	n/a	n/a
15	CEBPB	chr11:94135457-94135824	HepG2	liver:	n/a	n/a
16	ESR1	chr11:94135574-94135819	T-47D	breast:	n/a	chr11:94135697-94135714
17	FOSL2	chr11:94135539-94135875	HepG2	liver:	n/a	chr11:94135747-94135754 chr11:94135747-94135755

Variant related genes	Relation type
GPR83	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1014666	0.81[CEU][hapmap]
rs10831225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11020802	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11020803	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12224966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1257769	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1272743	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508784	0.81[CEU][hapmap]
rs3017077	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs472344	0.80[CEU][hapmap]
rs473297	0.81[CEU][hapmap]
rs474577	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs497763	0.84[CEU][hapmap]
rs500558	0.80[CEU][hapmap]
rs509723	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs509744	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs512150	0.84[CEU][hapmap]
rs516381	0.81[AFR][1000 genomes]
rs518640	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs521349	0.92[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs525057	0.80[CEU][hapmap]
rs525921	0.80[CEU][hapmap]
rs530569	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs535801	0.86[ASW][hapmap];0.86[CHD][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs540199	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56108804	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs563807	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs588701	1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59678918	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610899	0.80[CEU][hapmap]
rs625245	0.80[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs639311	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs641936	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6483341	0.81[CEU][hapmap]
rs654718	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs657249	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs680695	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs682213	0.81[CEU][hapmap]
rs684507	0.81[CEU][hapmap]
rs695093	0.80[CEU][hapmap]
rs948575	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][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	nsv523083	chr11:93962121-94150790	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832233	chr11:93981434-94158471	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs550255	RP11-685N10.1	cis	Stomach	GTEx
rs550255	MRE11A	cis	Thyroid	GTEx
rs550255	MAML2	cis	cerebellum	SCAN
rs550255	MRE11A	cis	Esophagus Muscularis	GTEx
rs550255	RP11-685N10.1	cis	Nerve Tibial	GTEx
rs550255	RP11-685N10.1	cis	lung	GTEx
rs550255	MRE11A	cis	Skin Sun Exposed Lower leg	GTEx
rs550255	RP11-685N10.1	cis	Muscle Skeletal	GTEx
rs550255	MRE11A	cis	Artery Tibial	GTEx
rs550255	MRE11A	cis	Artery Aorta	GTEx
rs550255	MRE11A	cis	parietal	SCAN
rs550255	RP11-685N10.1	cis	Adipose Subcutaneous	GTEx
rs550255	MRE11A	cis	Nerve Tibial	GTEx
rs550255	MRE11A	cis	Stomach	GTEx
rs550255	RP11-685N10.1	cis	Artery Aorta	GTEx
rs550255	MRE11A	cis	cerebellum	SCAN
rs550255	RP11-685N10.1	cis	Skin Sun Exposed Lower leg	GTEx
rs550255	MRE11A	cis	Adipose Subcutaneous	GTEx
rs550255	RP11-685N10.1	cis	Thyroid	GTEx
rs550255	MRE11A	Cis_1M	lymphoblastoid	RTeQTL
rs550255	MRE11A	cis	Heart Left Ventricle	GTEx
rs550255	RP11-685N10.1	cis	Artery Tibial	GTEx
rs550255	MRE11A	cis	Whole Blood	GTEx
rs550255	RP11-685N10.1	cis	Esophagus Mucosa	GTEx
rs550255	MRE11A	cis	lung	GTEx
rs550255	RP11-685N10.1	cis	Heart Left Ventricle	GTEx
rs550255	MRE11A	cis	Esophagus Mucosa	GTEx
rs550255	RP11-685N10.1	cis	Esophagus Muscularis	GTEx
rs550255	MAML2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94135000-94135800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:94135200-94135800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
3	chr11:94135200-94135800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:94135200-94136000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:94135200-94136000	Enhancers	HepG2	liver
6	chr11:94135200-94161400	Weak transcription	Placenta	Placenta
7	chr11:94135200-94162200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:94135400-94135800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:94135400-94135800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr11:94135400-94135800	Bivalent Enhancer	HMEC	breast
11	chr11:94135400-94135800	Bivalent Enhancer	NHEK	skin
12	chr11:94135400-94136000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:94135600-94135800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
14	chr11:94135600-94135800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:94135600-94135800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:94135600-94135800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:94135600-94136000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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