Variant report

Variant	rs9524017
Chromosome Location	chr13:94005805-94005806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:94004779..94008809-chr13:94017437..94020691,3	K562	blood:
2	chr13:94003388..94006279-chr13:94018446..94020737,2	K562	blood:
3	chr13:94004123..94006975-chr13:94011670..94013283,2	K562	blood:
4	chr13:93996122..93998219-chr13:94004133..94006443,2	K562	blood:
5	chr13:94000395..94002104-chr13:94003785..94006274,3	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11617476	1.00[JPT][hapmap]
rs1323974	0.88[ASW][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1323975	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1323984	0.81[GIH][hapmap]
rs1323985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1323986	0.81[GIH][hapmap]
rs1323988	1.00[JPT][hapmap]
rs1373835	1.00[JPT][hapmap]
rs1408209	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408219	1.00[JPT][hapmap]
rs1819341	0.87[AMR][1000 genomes]
rs1952361	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2225189	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2762095	1.00[JPT][hapmap]
rs2762097	1.00[JPT][hapmap]
rs2762100	1.00[JPT][hapmap]
rs2762106	1.00[JPT][hapmap]
rs2762107	1.00[JPT][hapmap]
rs2762109	1.00[JPT][hapmap]
rs2762110	1.00[JPT][hapmap]
rs2762111	1.00[JPT][hapmap]
rs2762114	1.00[JPT][hapmap]
rs2762116	1.00[JPT][hapmap]
rs2762117	1.00[JPT][hapmap]
rs2813608	1.00[JPT][hapmap]
rs2813609	1.00[JPT][hapmap]
rs2813610	1.00[JPT][hapmap]
rs2813615	1.00[JPT][hapmap]
rs35664727	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4142601	0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773741	1.00[JPT][hapmap]
rs4773742	1.00[JPT][hapmap]
rs6492659	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7324202	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7982827	1.00[JPT][hapmap]
rs7984266	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7985067	0.86[YRI][hapmap]
rs7988684	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7992679	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7994395	0.83[ASW][hapmap]
rs8001600	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs9301874	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9301875	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9524021	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561325	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561332	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs995810	0.88[ASW][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs995811	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv900919	chr13:93957816-94030693	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv530636	chr13:93997311-94281707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9524017	GPC6	cis	Liver	GTEx
rs9524017	HSS00257252	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93998800-94007000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr13:94004600-94006200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:94005200-94006000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links