Variant report

Variant	rs11264866
Chromosome Location	chr1:153987050-153987051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10127983	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs10559	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs10796986	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908557	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10908558	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs10908627	1.00[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs1110165	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs11264532	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs11264680	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs11264743	0.82[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs11264865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264875	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264886	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs11264895	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264964	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs11264974	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11265036	0.89[ASN][1000 genomes]
rs11265040	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11265049	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11265076	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11265082	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs11265099	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11265122	0.91[ASW][hapmap]
rs11581644	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs11586701	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11589857	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11590099	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12021641	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs12022158	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12022730	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12028398	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12032914	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs12033835	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap]
rs12041920	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12042562	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12042989	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12043350	0.82[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs12048137	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049128	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12401565	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs12403956	0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12408260	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes]
rs1572788	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs3748848	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs3791187	0.82[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs4521985	0.91[ASW][hapmap]
rs4845357	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs4845583	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4845600	0.91[ASW][hapmap]
rs4845601	0.91[ASW][hapmap]
rs58300038	0.87[ASN][1000 genomes]
rs61542760	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427457	0.89[ASN][1000 genomes]
rs6667928	0.91[ASW][hapmap]
rs6670019	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672856	0.91[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678826	0.91[ASW][hapmap]
rs6679907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680140	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs6701341	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];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6703545	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521303	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7537691	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7544502	0.91[ASN][1000 genomes]
rs7547663	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7552737	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8450	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs946682	0.91[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11264866	SLC27A3	cis	cerebellum	SCAN
rs11264866	SPRR2D	cis	parietal	SCAN
rs11264866	CRTC2	cis	cerebellum	SCAN
rs11264866	SLC25A44	cis	cerebellum	SCAN
rs11264866	SLC39A1	cis	cerebellum	SCAN
rs11264866	LASS2	cis	parietal	SCAN
rs11264866	CRTC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153968400-153988400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:153973600-153998000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:153986400-153987200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:153986600-153987800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:153986800-153987200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:153986800-153987200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:153986800-153987200	Enhancers	Stomach Mucosa	stomach
8	chr1:153986800-153987200	Enhancers	HepG2	liver
9	chr1:153986800-153987200	Enhancers	NHDF-Ad	bronchial
10	chr1:153986800-153987200	Enhancers	NHLF	lung

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