Variant report

Variant	rs1392129
Chromosome Location	chr1:56066714-56066715
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10493196	0.85[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10749702	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11206625	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11206629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11206636	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11206637	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11206638	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11206639	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11807964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12026971	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041985	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12086546	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12128337	0.80[EUR][1000 genomes]
rs12132336	0.92[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12139752	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12142554	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12401977	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1392128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392130	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1392131	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1392132	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1587432	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1604016	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17112402	0.85[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17417716	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56169646	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61776360	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61776375	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61776377	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6588566	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6669248	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6675850	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7513395	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7525515	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7544458	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7546899	0.96[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7555929	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7556008	0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56059600-56076000	Weak transcription	Aorta	Aorta
2	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:56065600-56066800	Enhancers	NHDF-Ad	bronchial
4	chr1:56065600-56067000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:56065600-56067000	Enhancers	Fetal Muscle Leg	muscle
6	chr1:56065600-56067400	Enhancers	Ovary	ovary
7	chr1:56066000-56067200	Enhancers	Fetal Lung	lung
8	chr1:56066200-56066800	Enhancers	Fetal Stomach	stomach
9	chr1:56066400-56066800	Enhancers	Fetal Kidney	kidney
10	chr1:56066600-56067400	Enhancers	Fetal Intestine Large	intestine

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