Variant report

Variant	rs12489949
Chromosome Location	chr3:59501828-59501829
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10510812	0.82[AFR][1000 genomes]
rs11130713	0.82[AFR][1000 genomes]
rs11130714	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11923741	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925209	0.82[AFR][1000 genomes]
rs11925279	0.82[AFR][1000 genomes]
rs12486826	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12487257	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12492287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492308	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12493195	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17275189	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17275950	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4679487	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56197311	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57042572	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58664036	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60365449	0.82[AFR][1000 genomes]
rs73837348	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73837355	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011181	chr3:58665373-59542339	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv536574	chr3:58665373-59542339	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv534257	chr3:58855959-59606464	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv998676	chr3:59485915-59519363	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv876836	chr3:59500394-59664687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59499600-59503200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:59500200-59503800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:59500600-59502200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:59500800-59502000	Enhancers	Brain Hippocampus Middle	brain
5	chr3:59501000-59502000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:59501000-59502000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:59501000-59502000	Enhancers	Brain Substantia Nigra	brain
8	chr3:59501000-59502000	Enhancers	Fetal Brain Female	brain
9	chr3:59501000-59502200	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:59501200-59502000	Enhancers	Brain Germinal Matrix	brain
11	chr3:59501200-59502000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:59501200-59502200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:59501200-59502800	Weak transcription	Primary T cells from cord blood	blood
14	chr3:59501200-59503600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:59501400-59502200	Enhancers	Brain Anterior Caudate	brain
16	chr3:59501400-59502800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:59501400-59503800	Enhancers	Fetal Lung	lung
18	chr3:59501600-59502000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:59501600-59502200	Enhancers	Dnd41	blood
20	chr3:59501600-59503000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:59501600-59503800	Enhancers	Fetal Kidney	kidney
22	chr3:59501800-59502200	Enhancers	HUES48 Cell Line	embryonic stem cell

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