Variant report

Variant	rs11176497
Chromosome Location	chr12:67355158-67355159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10878541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878545	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504304	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103105	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009062	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603384	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053250	chr12:67067995-67381411	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1044939	chr12:67207260-67377982	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1036984	chr12:67273098-67427543	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1054433	chr12:67302689-67357930	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv541523	chr12:67302689-67357930	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1040723	chr12:67329322-67396230	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv525987	chr12:67336812-67394408	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv559210	chr12:67339554-67398938	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1040543	chr12:67345920-67395598	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11176497	USP15	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67353000-67355600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:67353200-67355600	Enhancers	NHEK	skin
3	chr12:67353800-67355600	Enhancers	HMEC	breast
4	chr12:67354000-67355200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:67354000-67355200	Enhancers	Esophagus	oesophagus
6	chr12:67354000-67355200	Enhancers	Placenta	Placenta
7	chr12:67354000-67355400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:67354000-67355600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:67354000-67356400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:67354200-67355400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:67354200-67355800	Weak transcription	Primary T cells from cord blood	blood
12	chr12:67354400-67355200	Enhancers	H9 Cell Line	embryonic stem cell
13	chr12:67354400-67355400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:67354400-67356400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:67354600-67355200	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr12:67354600-67355400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr12:67354600-67355600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:67354800-67355200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:67355000-67355600	Weak transcription	ES-UCSF4 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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