Variant report

Variant	rs12797573
Chromosome Location	chr11:77255306-77255307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11237216	0.80[ASN][1000 genomes]
rs11603537	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs12788763	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12801662	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12807030	0.90[ASN][1000 genomes]
rs1945752	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2156843	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34576136	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34924092	0.84[ASN][1000 genomes]
rs35861083	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7118876	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3471175	chr11:77254184-77256204	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
9	esv3471163	chr11:77254238-77256158	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
10	esv3471152	chr11:77254260-77256146	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv3471186	chr11:77254344-77256077	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12797573	AQP11	cis	lymphoblastoid	seeQTL
rs12797573	KCTD21	cis	cerebellum	SCAN
rs12797573	KCTD21	cis	parietal	SCAN
rs12797573	RSF1	cis	cerebellum	SCAN
rs12797573	NDUFC2	cis	cerebellum	SCAN
rs12797573	AQP11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77249200-77258600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:77253800-77259200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:77253800-77259200	Weak transcription	HSMMtube	muscle
4	chr11:77253800-77259200	Weak transcription	Osteobl	bone
5	chr11:77254000-77259200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:77254400-77259200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:77254600-77259000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:77255000-77255400	Enhancers	Fetal Intestine Large	intestine
9	chr11:77255000-77255600	Enhancers	Fetal Intestine Small	intestine
10	chr11:77255200-77255400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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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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