Variant report

Variant	rs1966609
Chromosome Location	chr12:41624428-41624429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10506182	0.96[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10748266	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10748275	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10785150	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10785165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10785174	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10785177	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10879830	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879858	0.81[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs10879889	0.96[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11180421	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1346905	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1367600	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1367601	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1405548	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1431100	0.88[CEU][hapmap]
rs1431102	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1431103	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1431105	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431106	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431107	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431108	0.86[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1431109	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431110	0.82[EUR][1000 genomes]
rs1431111	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431114	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1431115	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1431116	0.81[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527086	0.81[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs1852461	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864612	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1870704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2043134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060053	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060054	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2060055	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2195706	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2195707	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405768	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2567034	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs281831	0.85[AMR][1000 genomes]
rs281837	0.84[AMR][1000 genomes]
rs2897227	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2897228	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2897229	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3911712	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4278570	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4506713	0.81[ASN][1000 genomes]
rs4768335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582280	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6582281	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6582282	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6582283	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7137842	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7296581	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7301200	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7304286	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7487688	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7956699	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961556	0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7961657	0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7963760	0.81[CEU][hapmap]
rs7980599	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs975602	0.81[CEU][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs9788073	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1966609	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41611800-41625200	Weak transcription	Aorta	Aorta
2	chr12:41621000-41625400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:41623000-41625000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:41623200-41635600	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:41623600-41637000	Weak transcription	Ovary	ovary
6	chr12:41623800-41624600	Enhancers	Brain Substantia Nigra	brain
7	chr12:41623800-41625000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr12:41624000-41625000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr12:41624000-41625200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:41624000-41625400	Enhancers	Brain Cingulate Gyrus	brain
11	chr12:41624400-41624800	Weak transcription	Brain Anterior Caudate	brain
12	chr12:41624400-41625000	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links