Variant report

Variant	rs10888529
Chromosome Location	chr1:153050654-153050655
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10888528	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1108410	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[EUR][1000 genomes]
rs11205179	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11205180	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11205181	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11205182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205185	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11205186	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11205187	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205188	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205189	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11485498	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11488175	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11576797	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11587269	0.84[CEU][hapmap]
rs11590835	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11812015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079087	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12082627	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12083211	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1415972	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs1500937	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1577960	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1995308	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs28924721	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs3737864	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4845513	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs55906223	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56158137	0.92[EUR][1000 genomes]
rs56412380	0.92[EUR][1000 genomes]
rs61811886	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61811902	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61811903	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587724	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587725	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660797	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660878	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6661059	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6661063	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6664380	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6670380	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675009	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6677674	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6680061	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683514	0.81[EUR][1000 genomes]
rs6686526	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6689066	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6689510	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698361	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7531076	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7532166	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7540609	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7543689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548977	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes]
rs7551791	0.83[AMR][1000 genomes];0.94[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	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv464017	chr1:153033406-153099345	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv547920	chr1:153033406-153099345	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv946395	chr1:153042430-153069958	Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3334814	chr1:153044548-153067651	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10888529	SPRR1B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153032200-153053400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:153050200-153050800	Enhancers	NHEK	skin

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