Variant report

Variant	rs9669757
Chromosome Location	chr12:41082268-41082269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1013929	0.91[ASN][1000 genomes]
rs10161138	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10161509	0.81[ASN][1000 genomes]
rs10735957	0.91[ASN][1000 genomes]
rs10748138	0.93[ASN][1000 genomes]
rs10748142	0.83[ASN][1000 genomes]
rs10748148	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784796	0.91[ASN][1000 genomes]
rs10784797	0.88[ASN][1000 genomes]
rs10784800	0.91[ASN][1000 genomes]
rs10879028	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10879031	0.86[ASN][1000 genomes]
rs10879079	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10879092	0.88[ASN][1000 genomes]
rs10879095	0.86[ASN][1000 genomes]
rs11177809	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11177862	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11177863	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11177886	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11177927	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11177961	0.83[ASN][1000 genomes]
rs11178000	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11178013	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11178015	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11178017	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11178018	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11178027	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11178067	0.88[ASN][1000 genomes]
rs11178070	0.90[CEU][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11178118	0.81[AMR][1000 genomes]
rs11178122	0.81[AMR][1000 genomes]
rs12296967	0.81[ASN][1000 genomes]
rs12367287	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12367641	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12372385	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1373425	0.91[ASN][1000 genomes]
rs1373426	0.91[ASN][1000 genomes]
rs1584090	0.84[ASN][1000 genomes]
rs1584094	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1584095	0.91[ASN][1000 genomes]
rs1584100	0.84[ASN][1000 genomes]
rs1816855	0.83[ASN][1000 genomes]
rs1918951	0.81[ASN][1000 genomes]
rs1992606	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2405290	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2405293	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2405294	0.91[ASN][1000 genomes]
rs2405295	0.83[ASN][1000 genomes]
rs3940638	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61915074	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61915099	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61915100	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61915101	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61915102	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6581905	0.86[ASN][1000 genomes]
rs7133642	0.88[ASN][1000 genomes]
rs7139243	0.81[AMR][1000 genomes]
rs7311914	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7312935	0.81[AMR][1000 genomes]
rs73267740	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953546	0.91[ASN][1000 genomes]
rs7960217	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7962501	0.91[ASN][1000 genomes]
rs7967298	0.86[ASN][1000 genomes]
rs7971056	0.83[ASN][1000 genomes]
rs7972371	0.90[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7974939	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs935224	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9783468	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv832378	chr12:40943111-41132305	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9669757	CNTN1	cis	normal skin	skin_eQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41081000-41085800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:41082000-41082400	Enhancers	Ovary	ovary
3	chr12:41082000-41082600	Enhancers	Brain Anterior Caudate	brain
4	chr12:41082000-41082600	Flanking Active TSS	A549	lung
5	chr12:41082200-41083200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:41082200-41085600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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