Variant report

Variant	rs10011112
Chromosome Location	chr4:110886306-110886307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110880113..110882132-chr4:110884747..110887034,2	MCF-7	breast:
2	chr4:110884465..110887295-chr4:110887593..110889209,2	K562	blood:
3	chr4:110884397..110887295-chr4:110887313..110889209,2	K562	blood:

Variant related genes	Relation type
ENSG00000138798	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10002971	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10014383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10017261	0.87[EUR][1000 genomes]
rs10023272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10029105	0.95[EUR][1000 genomes]
rs10029654	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs10213531	0.94[EUR][1000 genomes]
rs1024600	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10470911	1.00[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs10488881	1.00[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs11098056	0.91[EUR][1000 genomes]
rs11568903	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11568905	0.80[EUR][1000 genomes]
rs11568950	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11568972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11568994	0.87[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17238095	0.90[ASN][1000 genomes]
rs17253063	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17316633	0.90[ASN][1000 genomes]
rs2024114	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2067004	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs2190909	0.93[EUR][1000 genomes]
rs2237041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237045	0.94[EUR][1000 genomes]
rs2250616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282785	0.95[EUR][1000 genomes]
rs2298977	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2347136	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28437404	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28535066	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28540029	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28564978	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28629923	0.95[EUR][1000 genomes]
rs28672708	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28734982	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764861	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs3775967	0.95[EUR][1000 genomes]
rs3796945	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3796946	0.95[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs3822288	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4279279	0.92[EUR][1000 genomes]
rs4698755	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4698756	0.88[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4698800	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4698801	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs62327602	0.90[ASN][1000 genomes]
rs62327604	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6533481	0.95[EUR][1000 genomes]
rs6837717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6850557	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs7655579	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs7668520	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs881878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9307347	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9991904	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs9992755	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10011112	GAR1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110860600-110906600	Weak transcription	Psoas Muscle	Psoas
2	chr4:110869600-110888000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:110874400-110889000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:110875600-110909800	Weak transcription	Pancreas	Pancrea
5	chr4:110883400-110886400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:110884200-110893600	Weak transcription	Fetal Heart	heart
7	chr4:110885800-110897200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:110885800-110909800	Weak transcription	Left Ventricle	heart
9	chr4:110886000-110888000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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