Variant report

Variant	rs11161606
Chromosome Location	chr1:85853902-85853903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1001604	0.81[CEU][hapmap]
rs1006988	0.83[YRI][hapmap]
rs10489513	0.82[ASW][hapmap];0.81[CEU][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.84[AFR][1000 genomes]
rs11161607	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11161611	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1146382	0.81[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs12044537	0.81[CEU][hapmap];0.86[AFR][1000 genomes]
rs12047422	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12140103	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1498373	0.89[CEU][hapmap]
rs1554597	0.92[CEU][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs18582	0.89[CEU][hapmap]
rs1884139	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1975755	0.83[YRI][hapmap]
rs2011825	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2012683	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2177461	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2207368	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2268667	0.89[CEU][hapmap]
rs2300634	0.89[CEU][hapmap]
rs2300637	0.81[AMR][1000 genomes]
rs233047	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs233050	0.92[CEU][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs233053	0.82[ASW][hapmap];0.81[CEU][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.86[AFR][1000 genomes]
rs233054	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs233091	0.84[AMR][1000 genomes]
rs233093	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs233095	0.82[AMR][1000 genomes]
rs233099	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs233113	0.88[CEU][hapmap]
rs233115	0.84[CEU][hapmap]
rs233119	0.88[CEU][hapmap]
rs2474123	0.82[ASW][hapmap];0.85[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2840319	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2892888	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3768227	0.89[CEU][hapmap]
rs3920521	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3949301	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4949890	0.81[AMR][1000 genomes]
rs4949900	0.92[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs530006	0.85[GIH][hapmap]
rs58821561	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6576761	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6576763	0.81[CEU][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.84[AFR][1000 genomes]
rs6576764	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6576765	0.81[CEU][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap]
rs6576767	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6657817	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6671599	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66811655	0.81[AMR][1000 genomes]
rs6697083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6704103	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67611930	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72724606	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs729655	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521189	0.85[GIH][hapmap]
rs7525786	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7547571	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761601	0.89[CEU][hapmap]
rs997251	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	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
rs11161606	BCL10	cis	parietal	SCAN
rs11161606	GBP2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85839800-85864200	Weak transcription	Aorta	Aorta
2	chr1:85841200-85859800	Weak transcription	NH-A	brain
3	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
4	chr1:85845800-85859800	Weak transcription	NHLF	lung
5	chr1:85849400-85861600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:85849400-85863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:85850200-85854400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:85850800-85863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:85851600-85854600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:85852400-85863400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:85852400-85864200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:85852600-85860000	Weak transcription	Gastric	stomach
13	chr1:85852800-85854200	Weak transcription	Pancreas	Pancrea
14	chr1:85852800-85858800	Weak transcription	HSMM	muscle
15	chr1:85852800-85859800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:85853200-85861800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:85853400-85854000	Strong transcription	Osteobl	bone
18	chr1:85853400-85854400	Weak transcription	HepG2	liver
19	chr1:85853600-85854000	Weak transcription	Liver	Liver
20	chr1:85853600-85854000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:85853600-85854200	Enhancers	HUVEC	blood vessel
22	chr1:85853600-85861800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:85853800-85854800	Enhancers	Fetal Lung	lung
24	chr1:85853800-85858800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:85853800-85861600	Weak transcription	NHDF-Ad	bronchial
26	chr1:85853800-85864200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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