Variant report

Variant	rs4698800
Chromosome Location	chr4:110866508-110866509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110866088..110868993-chr4:110887686..110890288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138798	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10002971	0.86[EUR][1000 genomes]
rs10011112	0.96[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs10014383	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs10017261	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10023272	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10029105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029654	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10213531	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1024600	0.92[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10470911	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10488881	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098056	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11568903	0.90[EUR][1000 genomes]
rs11568905	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11568950	0.96[EUR][1000 genomes]
rs11568972	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs11568994	0.83[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs17253063	0.86[EUR][1000 genomes]
rs2024114	0.96[EUR][1000 genomes]
rs2067004	1.00[CEU][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2190909	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2237041	0.96[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs2237045	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250616	0.96[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2282785	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2298977	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2347136	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs28437404	0.96[EUR][1000 genomes]
rs28535066	0.94[EUR][1000 genomes]
rs28540029	0.98[EUR][1000 genomes]
rs28564978	0.98[EUR][1000 genomes]
rs28629923	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28672708	0.96[EUR][1000 genomes]
rs28734982	0.95[EUR][1000 genomes]
rs3764861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775967	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796945	0.98[EUR][1000 genomes]
rs3796946	1.00[CEU][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3822288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4279279	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4698755	1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4698756	0.92[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4698801	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62327604	0.96[EUR][1000 genomes]
rs6533481	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6837717	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs7655579	1.00[CEU][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7668520	1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7680062	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs881878	0.96[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs9307347	0.96[EUR][1000 genomes]
rs9992755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4698800	GAR1	cis	cerebellum	SCAN
rs4698800	CHMP4A	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110843000-110876200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:110852400-110873800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:110853800-110871200	Weak transcription	Left Ventricle	heart
4	chr4:110860600-110906600	Weak transcription	Psoas Muscle	Psoas
5	chr4:110860800-110874800	Weak transcription	Pancreas	Pancrea
6	chr4:110864000-110867000	Weak transcription	Liver	Liver
7	chr4:110864000-110871000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:110864000-110876400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:110866200-110867600	Enhancers	HepG2	liver
10	chr4:110866200-110870000	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:110866400-110866600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:110866400-110866600	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links