Variant report

Variant	rs11164661
Chromosome Location	chr1:103541331-103541332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11811018	0.81[CEU][hapmap]
rs12116763	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12116792	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12118796	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12119971	0.82[EUR][1000 genomes]
rs12121661	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12121762	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12122632	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12123205	0.85[EUR][1000 genomes]
rs12124555	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12127576	0.85[EUR][1000 genomes]
rs12128196	0.84[EUR][1000 genomes]
rs12129078	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130683	0.85[EUR][1000 genomes]
rs12131097	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12131383	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12131399	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12131769	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12131957	0.89[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12132053	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12135531	0.89[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12136577	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12136865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12138447	0.84[EUR][1000 genomes]
rs12140023	0.84[EUR][1000 genomes]
rs12140064	0.80[EUR][1000 genomes]
rs12140473	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12142411	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1337181	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1337184	0.81[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1337185	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1337187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1337189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375668	0.83[EUR][1000 genomes]
rs1415349	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1415353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1415354	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463035	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs17507469	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs17507967	0.82[MEX][hapmap]
rs1953672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1953673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1953674	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1975919	1.00[CHD][hapmap]
rs2126642	0.84[ASW][hapmap];0.85[MEX][hapmap]
rs2615996	1.00[CHD][hapmap]
rs2615997	1.00[CHD][hapmap]
rs2622839	1.00[CHD][hapmap]
rs2622847	1.00[CHD][hapmap]
rs2622857	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2622869	1.00[CHD][hapmap]
rs2622875	1.00[CHD][hapmap]
rs2622878	1.00[CHD][hapmap]
rs4489579	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4497231	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4908285	0.89[CEU][hapmap]
rs58982976	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61816504	0.82[EUR][1000 genomes]
rs61816509	0.85[EUR][1000 genomes]
rs61816511	0.85[EUR][1000 genomes]
rs61816512	0.85[EUR][1000 genomes]
rs61816513	0.85[EUR][1000 genomes]
rs61816515	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61816516	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61817081	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61817082	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61817084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61817085	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61817086	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6577346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577347	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6577349	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6668897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9645399	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv870600	chr1:103336601-103548497	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871475	chr1:103339272-103548497	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv871078	chr1:103352451-103548497	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv870995	chr1:103384610-103548497	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv871372	chr1:103403752-103564540	Strong transcription Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv871736	chr1:103409100-103548497	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv462783	chr1:103438795-103548497	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv546937	chr1:103438795-103548497	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv871365	chr1:103476179-103548497	Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103449200-103545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:103517400-103557200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:103517600-103550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:103519600-103543000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:103522400-103559000	Weak transcription	HSMM	muscle
6	chr1:103531200-103544200	Weak transcription	NH-A	brain
7	chr1:103538400-103548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:103539400-103544000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:103539600-103556600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:103539800-103546600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:103540400-103543000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:103540400-103545000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:103541200-103543400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:103541200-103545000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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