Variant report

Variant	rs546439
Chromosome Location	chr11:94135355-94135356
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	MAZ	chr11:94135331-94135505	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GPR83	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10741488	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10831222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10831227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11020774	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11523894	0.85[EUR][1000 genomes]
rs1257783	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2155209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2508783	0.83[TSI][hapmap]
rs3758787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824878	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459257	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491404	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs492073	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs514060	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs516037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs534402	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs538800	0.87[EUR][1000 genomes]
rs541090	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs554715	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556477	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs572372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs581449	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs583534	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs584531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592943	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs601391	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs604845	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs610611	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs618690	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs646130	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs546439	CWC15	cis	parietal	SCAN
rs546439	GPR83	cis	cerebellum	SCAN
rs546439	MRE11A	cis	parietal	SCAN
rs546439	MRE11A	cis	cerebellum	SCAN
rs546439	RP11-685N10.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94133800-94135400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr11:94133800-94135600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:94134400-94135600	Bivalent Enhancer	Liver	Liver
4	chr11:94134800-94135400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
5	chr11:94134800-94135400	Flanking Bivalent TSS/Enh	NHEK	skin
6	chr11:94135000-94135400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:94135000-94135600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
8	chr11:94135000-94135800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:94135200-94135400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr11:94135200-94135400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:94135200-94135400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:94135200-94135400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr11:94135200-94135600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:94135200-94135600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
15	chr11:94135200-94135600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr11:94135200-94135800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
17	chr11:94135200-94135800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:94135200-94136000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:94135200-94136000	Enhancers	HepG2	liver
20	chr11:94135200-94161400	Weak transcription	Placenta	Placenta
21	chr11:94135200-94162200	Weak transcription	Brain Inferior Temporal Lobe	brain

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