Variant report

Variant	rs7519540
Chromosome Location	chr1:56107974-56107975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1039294	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10493193	0.85[CEU][hapmap]
rs10493194	0.85[CEU][hapmap]
rs10493195	0.85[CEU][hapmap]
rs11206626	0.85[CEU][hapmap]
rs11206635	0.92[CEU][hapmap]
rs11206649	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11801001	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11805740	0.92[CEU][hapmap]
rs12116670	0.85[CEU][hapmap]
rs12117758	0.85[CEU][hapmap]
rs12124658	0.90[EUR][1000 genomes]
rs12125730	0.90[CEU][hapmap]
rs12139482	0.85[CEU][hapmap]
rs17418048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17418151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17418627	1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412634	1.00[JPT][hapmap]
rs4575120	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58623222	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6588567	0.85[CEU][hapmap]
rs6670673	0.85[CEU][hapmap]
rs6680818	0.85[CEU][hapmap]
rs6681925	0.85[CEU][hapmap]
rs6694786	0.92[CEU][hapmap]
rs7548272	0.85[CEU][hapmap]
rs7549716	0.85[CEU][hapmap]
rs7550575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769989	0.84[CEU][hapmap]

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	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
2	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
3	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
4	nsv526148	chr1:56101597-56146450	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56107000-56110800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:56107200-56108200	Weak transcription	Ovary	ovary
3	chr1:56107200-56110800	Weak transcription	NHEK	skin
4	chr1:56107200-56115800	Weak transcription	Aorta	Aorta
5	chr1:56107400-56110800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:56107400-56111400	Weak transcription	Fetal Kidney	kidney
7	chr1:56107600-56110200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:56107600-56110800	Weak transcription	HMEC	breast
9	chr1:56107600-56111200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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