Variant report

Variant	rs10879858
Chromosome Location	chr12:41599003-41599004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10506182	0.85[CEU][hapmap]
rs10748267	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10748275	0.83[EUR][1000 genomes]
rs10785165	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10785174	0.83[EUR][1000 genomes]
rs10785177	0.85[CEU][hapmap]
rs10785186	0.91[CHB][hapmap]
rs10879831	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879867	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10879889	0.88[CEU][hapmap]
rs11180421	0.85[CEU][hapmap]
rs11180448	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs12829840	0.86[ASN][1000 genomes]
rs1367600	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1367602	0.86[EUR][1000 genomes]
rs1405548	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1431104	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431110	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431111	0.81[EUR][1000 genomes]
rs1431112	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs1431113	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1431114	0.85[CEU][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs1431115	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs1431116	0.81[EUR][1000 genomes]
rs1461094	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1527086	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1852461	0.85[CEU][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs1864611	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864613	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870704	0.85[CEU][hapmap];0.81[MEX][hapmap];0.85[EUR][1000 genomes]
rs1966609	0.81[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs2043134	0.81[CEU][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs2060053	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2060054	0.81[EUR][1000 genomes]
rs2060055	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2163415	0.86[EUR][1000 genomes]
rs2163416	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2169299	0.87[EUR][1000 genomes]
rs281829	0.81[EUR][1000 genomes]
rs281832	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs281837	0.82[EUR][1000 genomes]
rs281839	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs281840	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs281841	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs281843	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3847980	0.92[CEU][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs3847981	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3858726	0.89[EUR][1000 genomes]
rs4238081	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767999	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768334	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs4768335	0.81[CEU][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes]
rs6582240	0.92[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7301200	0.83[EUR][1000 genomes]
rs7303285	0.92[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7304286	0.83[EUR][1000 genomes]
rs7305919	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs7342366	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs776560	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs776561	0.85[EUR][1000 genomes]
rs776562	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs776567	0.83[EUR][1000 genomes]
rs7954881	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956699	0.83[EUR][1000 genomes]
rs7963760	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788073	0.83[EUR][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
rs10879858	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41595400-41599200	Weak transcription	Aorta	Aorta
2	chr12:41598000-41599200	Enhancers	Colon Smooth Muscle	Colon
3	chr12:41599000-41599200	Flanking Active TSS	Ovary	ovary
4	chr12:41599000-41599200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr12:41599000-41599400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:41599000-41599400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:41599000-41599400	Enhancers	Primary B cells from peripheral blood	blood
8	chr12:41599000-41599400	Active TSS	Primary hematopoietic stem cells	blood
9	chr12:41599000-41599400	Active TSS	Brain Hippocampus Middle	brain
10	chr12:41599000-41599400	Active TSS	Brain Substantia Nigra	brain
11	chr12:41599000-41599400	Active TSS	Fetal Kidney	kidney
12	chr12:41599000-41599400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr12:41599000-41599600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:41599000-41599600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:41599000-41599600	Active TSS	Brain Angular Gyrus	brain
16	chr12:41599000-41599600	Active TSS	Brain Anterior Caudate	brain
17	chr12:41599000-41599600	Active TSS	Brain Cingulate Gyrus	brain
18	chr12:41599000-41599600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr12:41599000-41599600	Active TSS	Duodenum Mucosa	Duodenum
20	chr12:41599000-41599600	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr12:41599000-41599600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr12:41599000-41599600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr12:41599000-41599600	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr12:41599000-41599600	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr12:41599000-41599600	Active TSS	Right Atrium	heart
26	chr12:41599000-41599800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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