Variant report

Variant	rs10879422
Chromosome Location	chr12:72803953-72803954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 34 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10160913	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879429	0.86[EUR][1000 genomes]
rs10879430	0.86[EUR][1000 genomes]
rs10879431	0.86[EUR][1000 genomes]
rs10879432	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10879433	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10879435	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs10879438	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs10879440	0.84[AMR][1000 genomes]
rs10879441	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs11179130	1.00[ASN][1000 genomes]
rs11179139	1.00[ASN][1000 genomes]
rs11179175	1.00[ASN][1000 genomes]
rs11179183	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179189	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179199	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179236	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs11179242	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs11179251	0.84[AMR][1000 genomes]
rs11179252	0.84[AMR][1000 genomes]
rs11608809	1.00[ASN][1000 genomes]
rs1214895	1.00[CEU][hapmap]
rs12297047	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12301567	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12322905	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12367387	1.00[CEU][hapmap]
rs12368205	1.00[ASN][1000 genomes]
rs12372580	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1444602	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17111103	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111392	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs17111405	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs17111445	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs17111496	1.00[CEU][hapmap]
rs725409	1.00[ASN][1000 genomes]
rs73146948	1.00[ASN][1000 genomes]
rs73146969	1.00[ASN][1000 genomes]
rs9645830	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1052799	chr12:72752760-72820618	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv541533	chr12:72752760-72820618	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv832453	chr12:72778058-72966827	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:34)

SNP	Gene	Cis/trans	Tissue	Source
rs10879422	EEF1D	cis	Temporal Cortex	GTEx
rs10879422	NEFL	cis	Temporal Cortex	GTEx
rs10879422	SLC15A3	cis	Temporal Cortex	GTEx
rs10879422	RPS8	cis	Temporal Cortex	GTEx
rs10879422	SIPA1	cis	Temporal Cortex	GTEx
rs10879422	DBC1	cis	Temporal Cortex	GTEx
rs10879422	LPHN1	cis	Temporal Cortex	GTEx
rs10879422	C12orf75	cis	Temporal Cortex	GTEx
rs10879422	SFRS14	cis	Temporal Cortex	GTEx
rs10879422	GAP43	cis	Temporal Cortex	GTEx
rs10879422	VIPR1	cis	Temporal Cortex	GTEx
rs10879422	HERC5	cis	Temporal Cortex	GTEx
rs10879422	GIMAP8	cis	Temporal Cortex	GTEx
rs10879422	CNTNAP1	cis	Temporal Cortex	GTEx
rs10879422	RAPGEFL1	cis	Temporal Cortex	GTEx
rs10879422	RPL6	cis	Temporal Cortex	GTEx
rs10879422	CADM3	cis	Temporal Cortex	GTEx
rs10879422	ANKRD57	cis	Temporal Cortex	GTEx
rs10879422	ACVR1B	cis	Temporal Cortex	GTEx
rs10879422	ZNF280B	cis	Temporal Cortex	GTEx
rs10879422	DNM1	cis	Temporal Cortex	GTEx
rs10879422	SV2A	cis	Temporal Cortex	GTEx
rs10879422	FCHSD2	cis	Temporal Cortex	GTEx
rs10879422	GSDMD	cis	Temporal Cortex	GTEx
rs10879422	ATP5I	cis	Temporal Cortex	GTEx
rs10879422	RPS29	cis	Temporal Cortex	GTEx
rs10879422	UNC5A	cis	Temporal Cortex	GTEx
rs10879422	NRSN2	cis	Temporal Cortex	GTEx
rs10879422	KCNMA1	cis	Temporal Cortex	GTEx
rs10879422	SERBP1	cis	Temporal Cortex	GTEx
rs10879422	TM9SF4	cis	Temporal Cortex	GTEx
rs10879422	PODN	cis	Temporal Cortex	GTEx
rs10879422	COPG	cis	Temporal Cortex	GTEx
rs10879422	PPFIA2	cis	Temporal Cortex	GTEx

Chromatin state (count:0 , 50 per page) page:

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

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