Variant report

Variant	rs11174609
Chromosome Location	chr12:40380763-40380764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005956	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs10506140	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs10747971	0.84[JPT][hapmap]
rs10784338	0.92[JPT][hapmap]
rs10784353	0.92[JPT][hapmap]
rs10784356	0.92[JPT][hapmap]
rs10784359	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs10784369	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs10877891	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877990	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs10878049	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10878089	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11174702	0.81[ASN][1000 genomes]
rs11175024	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs12813098	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12823555	1.00[JPT][hapmap]
rs1482281	0.84[JPT][hapmap]
rs1586038	0.89[CHD][hapmap];0.92[JPT][hapmap]
rs1600866	0.92[JPT][hapmap]
rs1813122	0.84[JPT][hapmap]
rs2128277	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs2404352	0.92[JPT][hapmap]
rs2896825	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2896905	0.81[CHD][hapmap]
rs3925535	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4625545	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs4768200	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs4768204	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs530602	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550669	0.84[JPT][hapmap]
rs555740	0.84[JPT][hapmap]
rs6581504	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6650226	0.84[JPT][hapmap]
rs716268	1.00[JPT][hapmap]
rs7313209	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7313231	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7953129	0.92[JPT][hapmap]
rs7959498	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7960662	0.92[JPT][hapmap]
rs7964150	0.84[JPT][hapmap]
rs7970812	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9669240	0.82[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1052202	chr12:40322607-40406760	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11174609	PPHLN1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40364400-40391400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:40366400-40390200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:40379600-40380800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr12:40380400-40381000	Enhancers	NHEK	skin
5	chr12:40380600-40380800	Enhancers	Colon Smooth Muscle	Colon
6	chr12:40380600-40380800	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr12:40380600-40381000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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