Variant report

Variant	rs7967298
Chromosome Location	chr12:41087838-41087839
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1013929	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10161138	0.92[ASN][1000 genomes]
rs10735957	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10748138	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10748142	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748148	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784796	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784797	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784800	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10879019	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879028	0.96[ASN][1000 genomes]
rs10879031	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10879079	0.93[ASN][1000 genomes]
rs10879092	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879095	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10879131	0.84[ASN][1000 genomes]
rs11177809	0.93[ASN][1000 genomes]
rs11177862	0.99[ASN][1000 genomes]
rs11177863	0.99[ASN][1000 genomes]
rs11177886	0.96[ASN][1000 genomes]
rs11177927	0.96[ASN][1000 genomes]
rs11177954	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11177961	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11178000	0.96[ASN][1000 genomes]
rs11178013	0.96[ASN][1000 genomes]
rs11178015	0.96[ASN][1000 genomes]
rs11178017	0.96[ASN][1000 genomes]
rs11178018	0.96[ASN][1000 genomes]
rs11178027	0.96[ASN][1000 genomes]
rs11178050	0.90[ASN][1000 genomes]
rs11178067	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11178070	0.93[ASN][1000 genomes]
rs11178118	0.90[ASN][1000 genomes]
rs11178122	0.90[ASN][1000 genomes]
rs12367287	0.99[ASN][1000 genomes]
rs12367641	0.99[ASN][1000 genomes]
rs12367708	0.84[ASN][1000 genomes]
rs12372385	0.96[ASN][1000 genomes]
rs1373425	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1373426	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1584090	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1584094	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1584095	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1584100	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1596538	0.82[ASN][1000 genomes]
rs1816855	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1992606	0.99[ASN][1000 genomes]
rs2405293	0.99[ASN][1000 genomes]
rs2405294	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405295	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3940638	0.85[ASN][1000 genomes]
rs61915074	0.89[ASN][1000 genomes]
rs61915099	0.96[ASN][1000 genomes]
rs61915100	0.96[ASN][1000 genomes]
rs61915101	0.96[ASN][1000 genomes]
rs61915102	0.93[ASN][1000 genomes]
rs6581905	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133642	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7139243	0.90[ASN][1000 genomes]
rs7311914	0.89[ASN][1000 genomes]
rs7312935	0.90[ASN][1000 genomes]
rs7953546	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7960217	0.96[ASN][1000 genomes]
rs7961129	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7962501	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7971056	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972371	0.99[ASN][1000 genomes]
rs7974939	0.93[ASN][1000 genomes]
rs935224	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9669757	0.86[ASN][1000 genomes]
rs9783468	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7967298	CNTN1	cis	Esophagus Mucosa	GTEx
rs7967298	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41085600-41088000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:41085600-41088000	Active TSS	Fetal Brain Male	brain
3	chr12:41085600-41088400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:41085800-41088000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:41085800-41088000	Active TSS	Brain Anterior Caudate	brain
6	chr12:41087200-41088000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:41087200-41088200	Bivalent/Poised TSS	Fetal Brain Female	brain
8	chr12:41087200-41088600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr12:41087400-41088000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:41087400-41088000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
11	chr12:41087400-41088200	Active TSS	Brain Hippocampus Middle	brain
12	chr12:41087600-41088000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
13	chr12:41087600-41088000	Active TSS	Brain Substantia Nigra	brain
14	chr12:41087600-41088000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr12:41087600-41088000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:41087600-41088400	Active TSS	Brain Angular Gyrus	brain
17	chr12:41087600-41091600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:41087800-41088000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:41087800-41088000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr12:41087800-41088000	Enhancers	Adipose Nuclei	Adipose
21	chr12:41087800-41088000	Bivalent Enhancer	Fetal Lung	lung
22	chr12:41087800-41088000	Enhancers	HMEC	breast
23	chr12:41087800-41088400	Enhancers	NHEK	skin
24	chr12:41087800-41089000	Flanking Active TSS	A549	lung
25	chr12:41087800-41091400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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