Variant report

Variant	rs7954772
Chromosome Location	chr12:47217940-47217941
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11183619	0.86[YRI][hapmap]
rs4447249	0.86[YRI][hapmap]
rs4587804	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7953215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963364	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7963399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963807	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968752	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7973308	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7974413	0.94[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7954772	ANP32D	cis	cerebellum	SCAN
rs7954772	C12orf68	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47211600-47219400	Weak transcription	Psoas Muscle	Psoas
2	chr12:47216000-47219200	Enhancers	HepG2	liver
3	chr12:47216200-47218200	Weak transcription	HSMM	muscle
4	chr12:47216600-47219200	Weak transcription	HSMMtube	muscle
5	chr12:47217400-47220200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:47217600-47219200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:47217800-47218000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:47217800-47218400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr12:47217800-47218800	Flanking Active TSS	Liver	Liver
10	chr12:47217800-47219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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