Variant report

Variant	rs12368659
Chromosome Location	chr12:48562299-48562300
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48549682..48552268-chr12:48561692..48563746,2	K562	blood:

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10875716	0.81[CEU][hapmap]
rs10875718	0.80[CEU][hapmap]
rs10875719	0.80[CEU][hapmap]
rs10875743	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10875749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10875763	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1107654	1.00[CHB][hapmap]
rs11168351	0.81[CEU][hapmap]
rs11168408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs11168428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168437	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs11168441	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11168460	1.00[CHB][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs12099462	0.81[EUR][1000 genomes]
rs12228750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12816820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1476607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2054905	1.00[CHB][hapmap]
rs3087716	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3997	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4760612	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap]
rs4760679	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs6580650	0.92[CEU][hapmap]
rs6580654	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7139330	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7297824	1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs7301003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7307566	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs7315820	1.00[CHB][hapmap];0.83[AFR][1000 genomes]
rs7486941	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs7487682	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7971880	0.81[CEU][hapmap]
rs7975632	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs8716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs973398	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs9971924	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv976608	chr12:48558446-48563571	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12368659	RP1-228P16.1	cis	Artery Tibial	GTEx
rs12368659	H1FNT	cis	Muscle Skeletal	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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