Variant report

Variant	rs1992606
Chromosome Location	chr12:41086817-41086818
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1013929	0.88[ASN][1000 genomes]
rs10161138	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10735957	0.88[ASN][1000 genomes]
rs10748138	0.91[ASN][1000 genomes]
rs10748142	0.96[ASN][1000 genomes]
rs10748148	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10784796	0.88[ASN][1000 genomes]
rs10784797	0.85[ASN][1000 genomes]
rs10784800	0.88[ASN][1000 genomes]
rs10879019	0.83[ASN][1000 genomes]
rs10879028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879031	0.84[ASN][1000 genomes]
rs10879079	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879092	0.86[ASN][1000 genomes]
rs10879095	0.83[ASN][1000 genomes]
rs10879131	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11177809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11177862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11177863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11177886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11177927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11177961	0.80[ASN][1000 genomes]
rs11178000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178017	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178027	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178050	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11178067	0.86[ASN][1000 genomes]
rs11178070	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11178118	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11178122	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12367287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367641	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367708	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12372385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373425	0.88[ASN][1000 genomes]
rs1373426	0.88[ASN][1000 genomes]
rs1584090	0.83[ASN][1000 genomes]
rs1584094	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1584095	0.88[ASN][1000 genomes]
rs1584100	0.83[ASN][1000 genomes]
rs1596538	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1816855	0.96[ASN][1000 genomes]
rs1899829	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2405293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405294	0.88[ASN][1000 genomes]
rs2405295	0.96[ASN][1000 genomes]
rs3940638	0.87[ASN][1000 genomes]
rs61915074	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61915099	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915100	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915101	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61915102	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581905	0.99[ASN][1000 genomes]
rs7133642	0.86[ASN][1000 genomes]
rs7139243	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311914	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7312935	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73267740	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7953546	0.88[ASN][1000 genomes]
rs7960217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961129	0.91[ASN][1000 genomes]
rs7962501	0.88[ASN][1000 genomes]
rs7967298	0.99[ASN][1000 genomes]
rs7971056	0.96[ASN][1000 genomes]
rs7972371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935224	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9669757	0.84[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9783468	0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1992606	CNTN1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41085400-41087200	Active TSS	Brain Angular Gyrus	brain
2	chr12:41085600-41087000	Active TSS	Fetal Brain Female	brain
3	chr12:41085600-41087600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:41085600-41087600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
5	chr12:41085600-41087600	Active TSS	Colon Smooth Muscle	Colon
6	chr12:41085600-41087600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:41085600-41087600	Active TSS	NHDF-Ad	bronchial
8	chr12:41085600-41087800	Bivalent/Poised TSS	Fetal Lung	lung
9	chr12:41085600-41088000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:41085600-41088000	Active TSS	Fetal Brain Male	brain
11	chr12:41085600-41088400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:41085800-41087000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:41085800-41087000	Active TSS	Ovary	ovary
14	chr12:41085800-41087000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
15	chr12:41085800-41087200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr12:41085800-41087200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
17	chr12:41085800-41087200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
18	chr12:41085800-41087400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:41085800-41087400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:41085800-41087400	Active TSS	Aorta	Aorta
21	chr12:41085800-41087400	Enhancers	Fetal Heart	heart
22	chr12:41085800-41087400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr12:41085800-41087400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
24	chr12:41085800-41087400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
25	chr12:41085800-41087600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr12:41085800-41087600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:41085800-41087600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:41085800-41087600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:41085800-41087600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr12:41085800-41087800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:41085800-41087800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:41085800-41087800	Active TSS	Fetal Kidney	kidney
33	chr12:41085800-41087800	Active TSS	A549	lung
34	chr12:41085800-41088000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:41085800-41088000	Active TSS	Brain Anterior Caudate	brain
36	chr12:41086000-41087000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:41086000-41087000	Bivalent/Poised TSS	Fetal Thymus	thymus
38	chr12:41086000-41087000	Active TSS	Gastric	stomach
39	chr12:41086000-41087000	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion
40	chr12:41086000-41087000	Active TSS	Right Atrium	heart
41	chr12:41086000-41087200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:41086000-41087200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:41086000-41087200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:41086000-41087200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr12:41086000-41087200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr12:41086000-41087400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr12:41086000-41087400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:41086000-41087400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:41086000-41087400	Bivalent Enhancer	Placenta	Placenta
50	chr12:41086000-41087600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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