Variant report

Variant	rs425149
Chromosome Location	chr1:76997845-76997846
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11577619	1.00[ASN][1000 genomes]
rs12117865	1.00[CHB][hapmap]
rs12239615	1.00[CHB][hapmap]
rs1369805	1.00[CHB][hapmap]
rs17099155	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17631994	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs178355	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs192875	1.00[ASN][1000 genomes]
rs2647392	1.00[CHB][hapmap]
rs315060	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs315061	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs315062	1.00[ASN][1000 genomes]
rs315072	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs315073	1.00[ASN][1000 genomes]
rs315074	1.00[ASN][1000 genomes]
rs315075	1.00[ASN][1000 genomes]
rs315078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs315079	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs315081	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341029	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs402112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4300268	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4336900	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4492668	1.00[ASN][1000 genomes]
rs4598537	1.00[CHB][hapmap]
rs6593544	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7541103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7544201	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7547383	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv462006	chr1:76826279-77042405	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv546585	chr1:76826279-77042405	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv997827	chr1:76929028-77201457	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv462039	chr1:76948044-77019597	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv470718	chr1:76948044-77019597	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv546588	chr1:76948044-77019597	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv462050	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv462062	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv462073	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv546589	chr1:76948044-77019986	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv428774	chr1:76971045-77075766	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs425149	NEXN	cis	cerebellum	SCAN
rs425149	ZZZ3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76996400-76999200	Weak transcription	Primary B cells from cord blood	blood
2	chr1:76997000-76999200	Enhancers	Brain Substantia Nigra	brain
3	chr1:76997400-76998800	Enhancers	Brain Hippocampus Middle	brain
4	chr1:76997600-76998600	Weak transcription	Adipose Nuclei	Adipose
5	chr1:76997600-77010800	Weak transcription	Fetal Intestine Small	intestine
6	chr1:76997800-76998000	Enhancers	Brain Angular Gyrus	brain
7	chr1:76997800-76999000	Enhancers	Brain Cingulate Gyrus	brain

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