Variant report

Variant	rs10778358
Chromosome Location	chr12:105312216-105312217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1002803	0.86[CHD][hapmap];0.85[GIH][hapmap]
rs10507184	0.86[ASW][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs10746008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10778355	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861294	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112253	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1155994	0.81[ASN][1000 genomes]
rs11610388	0.82[ASN][1000 genomes]
rs1389612	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1565813	0.86[ASW][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs2131806	0.80[GIH][hapmap]
rs2248012	0.90[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs2248986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2264892	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453155	0.83[GIH][hapmap]
rs2453156	0.84[CHB][hapmap]
rs2453161	0.83[CHD][hapmap]
rs2453166	0.86[ASW][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs2463018	0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs2463440	0.86[CHD][hapmap]
rs2463441	0.83[CHD][hapmap]
rs2468089	0.82[GIH][hapmap]
rs2468092	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2468105	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2468109	0.83[CHD][hapmap]
rs2468337	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2730291	0.86[CHD][hapmap];0.85[GIH][hapmap]
rs4076550	0.86[CEU][hapmap]
rs4334113	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4388976	0.90[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4393404	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[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];0.92[ASN][1000 genomes]
rs4964310	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs6539170	0.86[ASW][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs6539171	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs703681	0.85[CHD][hapmap]
rs7135015	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[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];0.93[ASN][1000 genomes]
rs7138686	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7309240	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73193606	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7967503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9668618	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs996294	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10778358	C12orf23	cis	parietal	SCAN
rs10778358	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:105290800-105331600	Weak transcription	Gastric	stomach
3	chr12:105293600-105321600	Weak transcription	A549	lung
4	chr12:105297400-105323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:105297600-105323400	Weak transcription	Aorta	Aorta
6	chr12:105297800-105313000	Weak transcription	Fetal Stomach	stomach
7	chr12:105298200-105314600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:105300400-105323200	Weak transcription	Pancreas	Pancrea
9	chr12:105304400-105324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:105304600-105315000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:105304800-105313800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:105304800-105314800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:105308800-105314800	Weak transcription	Liver	Liver

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