Variant report

Variant	rs11164663
Chromosome Location	chr1:103548497-103548498
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1012281	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10493986	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs10874666	0.84[EUR][1000 genomes]
rs10874667	0.84[EUR][1000 genomes]
rs10874669	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10874670	0.84[EUR][1000 genomes]
rs10874674	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164640	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11164643	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11164655	0.81[EUR][1000 genomes]
rs11164664	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586849	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs12057584	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12062184	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs12064011	0.84[EUR][1000 genomes]
rs12064766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12076769	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12078741	0.86[EUR][1000 genomes]
rs12084574	0.84[EUR][1000 genomes]
rs12084902	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12117071	1.00[CHB][hapmap]
rs12118250	1.00[CHB][hapmap]
rs12121498	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12121824	1.00[CHB][hapmap]
rs12121894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs12123005	0.84[EUR][1000 genomes]
rs12125432	0.84[EUR][1000 genomes]
rs12126868	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12130285	1.00[CHB][hapmap]
rs12130848	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133515	1.00[CHB][hapmap]
rs12135438	1.00[CHB][hapmap]
rs12140939	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12141988	1.00[CHB][hapmap]
rs12142333	0.84[EUR][1000 genomes]
rs12145801	1.00[CHB][hapmap]
rs12145872	1.00[CHB][hapmap]
rs1337195	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs1415363	1.00[CHD][hapmap]
rs1577803	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17127270	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2045819	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2376260	1.00[CHB][hapmap]
rs3861742	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4391683	1.00[CHB][hapmap]
rs4908287	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs4908288	1.00[CHB][hapmap]
rs4908290	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs6577351	1.00[GIH][hapmap]
rs6674315	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74110526	0.84[EUR][1000 genomes]
rs7513552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7517160	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537288	0.88[CEU][hapmap];1.00[GIH][hapmap]
rs7543082	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv932937	chr1:103548172-103548502	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
13	nsv931600	chr1:103548397-104161031	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103517400-103557200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:103517600-103550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:103522400-103559000	Weak transcription	HSMM	muscle
4	chr1:103538400-103548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:103539600-103556600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:103542400-103549600	Weak transcription	Fetal Heart	heart
7	chr1:103544000-103570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:103544200-103551800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:103545000-103566800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:103546200-103556000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:103546600-103549200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:103548000-103564400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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