Variant report

Variant	rs2705125
Chromosome Location	chr12:48881891-48881892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48880029..48882865-chr12:48884102..48887272,3	K562	blood:
2	chr12:48880500..48882865-chr12:48883478..48886344,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANP32D-2	chr12:48881610-48882283	NONHSAT028005
2	lnc-ANP32D-2	chr12:48881729-48882191	NONHSAT028006

Variant related genes	Relation type
ENSG00000177627	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10747550	0.93[CEU][hapmap]
rs10783262	0.92[CEU][hapmap]
rs1895999	0.93[CEU][hapmap]
rs2252234	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2468351	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2468939	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705131	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2705134	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2705156	0.81[AFR][1000 genomes]
rs2731063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731074	0.81[YRI][hapmap]
rs2731092	0.89[CHB][hapmap]
rs2731096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731099	0.81[CHB][hapmap]
rs2731105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731106	0.82[JPT][hapmap]
rs2731111	0.82[AFR][1000 genomes]
rs2732447	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2956465	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2956466	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34478996	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34801828	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4369449	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4492859	0.93[CEU][hapmap]
rs4635128	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139348	0.89[CHB][hapmap]
rs71464905	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7309958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956260	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv975484	chr12:48881500-48882416	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2705125	C12orf54	cis	multi-tissue	Pritchard
rs2705125	C12orf54	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48880800-48882000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:48880800-48882400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:48880800-48882400	Weak transcription	GM12878-XiMat	blood
4	chr12:48881000-48882800	Enhancers	NHEK	skin
5	chr12:48881600-48883800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:48881600-48884000	Enhancers	HMEC	breast
7	chr12:48881800-48882000	Enhancers	Esophagus	oesophagus

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