Variant report

Variant	rs2209829
Chromosome Location	chr13:93132560-93132561
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	FOXA1	chr13:93132315-93132722	HepG2	liver:	n/a	chr13:93132547-93132562

Variant related genes	Relation type
GPC5-IT1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1180900	0.91[ASW][hapmap];0.81[CHB][hapmap]
rs12874576	0.87[AFR][1000 genomes]
rs1360671	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1413191	0.90[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap]
rs17436336	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap]
rs1855367	0.90[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.80[YRI][hapmap]
rs2149059	0.81[CHB][hapmap]
rs2209832	0.91[ASW][hapmap]
rs2374031	0.90[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2780744	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs449674	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.81[MEX][hapmap];0.80[YRI][hapmap]
rs4542527	0.92[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs55803730	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6492610	0.93[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6492611	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs722178	0.90[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs727986	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7490474	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7998089	0.90[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.80[YRI][hapmap]
rs9516089	0.81[CHB][hapmap]
rs9556183	0.92[CHB][hapmap];0.85[JPT][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9561079	0.90[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9561080	0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.85[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	nsv832680	chr13:93021114-93181489	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv977269	chr13:93125018-93132725	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93131800-93133400	Enhancers	Fetal Intestine Small	intestine
2	chr13:93132200-93133400	Enhancers	Fetal Intestine Large	intestine

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