Variant report

Variant	rs12488948
Chromosome Location	chr3:50969965-50969966
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50968160..50970692-chr3:50972135..50973895,2	K562	blood:
2	chr3:50965494..50967505-chr3:50968785..50971501,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11712367	0.82[CHD][hapmap]
rs11917538	0.82[CHD][hapmap]
rs12485524	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486828	0.91[ASN][1000 genomes]
rs12487821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12488700	0.93[JPT][hapmap]
rs12488831	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490502	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12490519	0.91[ASN][1000 genomes]
rs12491206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12491402	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492367	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12492850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494214	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12494708	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12494776	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495399	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12496601	0.89[ASN][1000 genomes]
rs12496621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12497067	0.90[ASN][1000 genomes]
rs13061003	0.82[CHD][hapmap]
rs13080170	0.82[CHD][hapmap]
rs17051468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2125368	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2262847	0.94[ASN][1000 genomes]
rs2355707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4073739	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4078296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4323036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4356848	0.82[CHD][hapmap]
rs4443210	0.82[CHD][hapmap]
rs4485709	0.82[CHD][hapmap]
rs4688695	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4688696	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4688697	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4688752	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4927961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs4927975	0.86[YRI][hapmap]
rs56844171	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58356214	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58720544	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60184902	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60552386	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60602904	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60882641	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60917457	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61557316	0.82[ASN][1000 genomes]
rs61627377	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61676409	0.88[ASN][1000 genomes]
rs6446222	0.81[CHD][hapmap]
rs6446239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772197	0.82[CHD][hapmap]
rs6795573	0.82[CHD][hapmap]
rs72937251	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72937253	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72937262	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72937265	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72937299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72939228	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72942530	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72942567	0.91[ASN][1000 genomes]
rs7372342	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7427526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7427615	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7433217	0.81[CHD][hapmap]
rs7614482	0.82[CHD][hapmap]
rs7627266	0.82[CHD][hapmap]
rs7638082	0.82[CHD][hapmap]
rs9825535	0.82[CHD][hapmap]
rs9865532	0.82[CHD][hapmap]
rs9869945	0.82[CHD][hapmap]
rs9875961	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1004881	chr3:50900793-51032918	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv536568	chr3:50900793-51032918	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1803890	chr3:50966037-50987194	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12488948	HEMK1	cis	multi-tissue	Pritchard
rs12488948	HEMK1	cis	lymphoblastoid	seeQTL
rs12488948	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50960000-50973000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:50964600-50972600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:50966800-50971400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:50968200-50972600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:50968400-50973000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:50969800-50972800	Weak transcription	Brain Inferior Temporal Lobe	brain

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