Variant report

Variant	rs11175024
Chromosome Location	chr12:40463950-40463951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1005956	0.91[JPT][hapmap]
rs1031996	0.90[MEX][hapmap]
rs10506140	0.91[JPT][hapmap]
rs10747971	0.84[JPT][hapmap]
rs10784338	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs10784353	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10784356	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10784359	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784369	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10877891	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10877990	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs10878031	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10878049	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174609	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11174809	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11174812	0.90[ASN][1000 genomes]
rs11174813	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12813098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823555	0.88[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1463719	0.90[MEX][hapmap]
rs1472118	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1482281	0.84[JPT][hapmap]
rs1586038	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1600866	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1813122	0.84[JPT][hapmap]
rs2128275	0.88[ASN][1000 genomes]
rs2128277	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2404352	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638245	0.90[MEX][hapmap]
rs2638266	0.82[CEU][hapmap]
rs2896825	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2896905	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3925535	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];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4625545	0.94[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4767960	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768200	0.90[JPT][hapmap]
rs4768204	0.91[JPT][hapmap]
rs530602	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs550669	0.84[JPT][hapmap]
rs555740	0.84[JPT][hapmap]
rs6581504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6650226	0.84[JPT][hapmap]
rs7139216	0.86[ASN][1000 genomes]
rs716268	0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313209	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs7313231	0.93[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7953129	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7959498	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[ASN][1000 genomes]
rs7960662	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7964150	0.84[JPT][hapmap]
rs7970812	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs878010	0.90[MEX][hapmap]
rs900253	0.85[MEX][hapmap]
rs9669240	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];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11175024	AC079630.2	cis	Esophagus Mucosa	GTEx
rs11175024	SLC2A13	cis	parietal	SCAN
rs11175024	LRRK2	cis	parietal	SCAN
rs11175024	ZCRB1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40453800-40487400	Weak transcription	Left Ventricle	heart
2	chr12:40457600-40471600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:40460400-40464000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:40463200-40464000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:40463200-40464000	Enhancers	Stomach Smooth Muscle	stomach
6	chr12:40463200-40464600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:40463400-40464600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr12:40463800-40464400	Enhancers	Colon Smooth Muscle	Colon

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