Variant report

Variant	rs12432214
Chromosome Location	chr14:39350566-39350567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10483546	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11157021	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11157022	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12433439	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108400	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes]
rs17108424	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17108452	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17401680	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73281372	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv564416	chr14:39140536-39440106	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv470631	chr14:39153764-39440106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv932194	chr14:39173578-39411337	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12432214	RALGAPA1	cis	parietal	SCAN
rs12432214	BRMS1L	cis	cerebellum	SCAN
rs12432214	NKX2-1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39347000-39351600	Enhancers	Brain Hippocampus Middle	brain
2	chr14:39349400-39350800	Enhancers	Fetal Lung	lung
3	chr14:39349600-39350600	Enhancers	Brain Cingulate Gyrus	brain
4	chr14:39349600-39350600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr14:39349800-39350600	Genic enhancers	Brain Substantia Nigra	brain
6	chr14:39349800-39350800	Enhancers	Fetal Stomach	stomach
7	chr14:39349800-39351200	Enhancers	HUVEC	blood vessel
8	chr14:39349800-39351600	Enhancers	Adipose Nuclei	Adipose
9	chr14:39350000-39350600	Enhancers	Small Intestine	intestine
10	chr14:39350000-39350800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr14:39350000-39350800	Enhancers	Fetal Intestine Large	intestine
12	chr14:39350000-39350800	Enhancers	Fetal Kidney	kidney
13	chr14:39350200-39350800	Enhancers	Brain Anterior Caudate	brain
14	chr14:39350400-39350600	Flanking Bivalent TSS/Enh	HepG2	liver

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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