Variant report

Variant	rs1460490
Chromosome Location	chr4:21470582-21470583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10516385	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10516386	1.00[CEU][hapmap]
rs10516388	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs10516389	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11942476	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13101628	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13102279	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13103488	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13104819	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13108860	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13109655	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13109855	0.81[CEU][hapmap]
rs13121386	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13122564	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13122807	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13127669	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13128830	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13129400	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13129501	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13129942	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13129962	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13135994	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13136002	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13136234	1.00[CEU][hapmap]
rs13137136	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13143135	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13144924	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13145021	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13145622	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13149579	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13150965	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1460488	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1460489	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1495501	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1495502	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1495503	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17464578	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17464752	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17464793	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17464828	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17465022	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17465591	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17523841	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17523876	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17524637	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17524672	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17524686	1.00[CEU][hapmap]
rs17524714	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17524784	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17524952	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17525063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2874930	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs3132	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs34222306	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34339769	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34836460	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34900760	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35032154	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35733464	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35854475	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35895330	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66601179	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66652160	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66739930	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66773055	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66993458	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67306339	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67949357	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67990405	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68049217	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs68116688	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6843022	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6843295	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71607078	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73249592	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73252219	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7441592	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9685466	1.00[CEU][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014062	chr4:21270358-21479027	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv829879	chr4:21418568-21611002	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv998481	chr4:21421945-21608805	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv593800	chr4:21456023-21471568	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA miRNA	n/a	inside rSNPs	n/a
6	nsv593804	chr4:21469139-21477084	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21469600-21471600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:21469800-21471400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:21470200-21470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:21470200-21471600	Weak transcription	HMEC	breast
5	chr4:21470400-21470600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:21470400-21470600	Enhancers	Brain Hippocampus Middle	brain

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