Variant report

Variant	rs11178122
Chromosome Location	chr12:41128378-41128379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1013929	0.86[ASN][1000 genomes]
rs10161138	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10735957	0.86[ASN][1000 genomes]
rs10748138	0.83[ASN][1000 genomes]
rs10748142	0.93[ASN][1000 genomes]
rs10748148	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784796	0.86[ASN][1000 genomes]
rs10784797	0.83[ASN][1000 genomes]
rs10784800	0.86[ASN][1000 genomes]
rs10879028	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879031	0.81[ASN][1000 genomes]
rs10879079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879092	0.88[ASN][1000 genomes]
rs10879095	0.91[ASN][1000 genomes]
rs10879131	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11177809	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11177862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11177863	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11177886	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11177927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178000	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178013	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178015	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178017	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178018	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178027	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178050	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178067	0.88[ASN][1000 genomes]
rs11178070	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367287	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12367641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12367708	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12372385	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1373425	0.86[ASN][1000 genomes]
rs1373426	0.86[ASN][1000 genomes]
rs1584090	0.91[ASN][1000 genomes]
rs1584094	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1584095	0.86[ASN][1000 genomes]
rs1584100	0.91[ASN][1000 genomes]
rs1596538	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1816855	0.93[ASN][1000 genomes]
rs1899829	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1992606	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2405293	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2405294	0.86[ASN][1000 genomes]
rs2405295	0.93[ASN][1000 genomes]
rs61915074	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61915099	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61915100	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61915101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61915102	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581905	0.90[ASN][1000 genomes]
rs7133642	0.88[ASN][1000 genomes]
rs7139243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311914	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7312935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73267740	0.82[AMR][1000 genomes]
rs7953546	0.86[ASN][1000 genomes]
rs7960217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961129	0.88[ASN][1000 genomes]
rs7962501	0.86[ASN][1000 genomes]
rs7967298	0.90[ASN][1000 genomes]
rs7971056	0.93[ASN][1000 genomes]
rs7972371	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7974939	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935224	0.91[JPT][hapmap]
rs9669757	0.89[CEU][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs9783468	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv2751098	chr12:41082399-41180235	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1044513	chr12:41091822-41175151	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv558696	chr12:41092666-41172010	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11178122	CNTN1	cis	normal skin	skin_eQTL
rs11178122	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41122800-41129600	Weak transcription	A549	lung
2	chr12:41126200-41130000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr12:41127400-41128400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr12:41127600-41128400	Enhancers	H9 Cell Line	embryonic stem cell
5	chr12:41127600-41128400	Enhancers	Brain Anterior Caudate	brain
6	chr12:41127600-41128800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:41127600-41128800	Enhancers	Brain Germinal Matrix	brain
8	chr12:41127800-41128400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:41127800-41128400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:41127800-41128600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:41128000-41128400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr12:41128000-41128400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr12:41128200-41128400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr12:41128200-41128400	Enhancers	Aorta	Aorta
15	chr12:41128200-41129800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr12:41128200-41130000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr12:41128200-41130000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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