Variant report

Variant	rs7669988
Chromosome Location	chr4:78681755-78681756
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10005741	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10007837	1.00[ASN][1000 genomes]
rs10222901	0.95[ASN][1000 genomes]
rs1039403	0.89[ASN][1000 genomes]
rs1039467	0.91[AMR][1000 genomes]
rs10856982	0.95[ASN][1000 genomes]
rs11097935	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1156059	0.91[ASN][1000 genomes]
rs11721383	0.87[AMR][1000 genomes]
rs11723029	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11723221	0.90[AMR][1000 genomes]
rs11727993	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11729703	0.87[AMR][1000 genomes]
rs11730329	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11730403	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11732039	0.91[AMR][1000 genomes]
rs11733759	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11734428	0.91[AMR][1000 genomes]
rs11939576	0.81[ASN][1000 genomes]
rs12510593	0.85[ASN][1000 genomes]
rs12643960	0.93[ASN][1000 genomes]
rs13105201	0.89[ASN][1000 genomes]
rs13111592	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118459	1.00[ASN][1000 genomes]
rs13128914	0.89[ASN][1000 genomes]
rs13131896	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13137909	0.95[ASN][1000 genomes]
rs13138341	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13144225	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13144226	0.95[ASN][1000 genomes]
rs1402626	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1501373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1502880	0.81[AMR][1000 genomes]
rs1521419	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1553386	0.91[AMR][1000 genomes]
rs1554457	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002823	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002824	0.81[ASN][1000 genomes]
rs17002825	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002828	0.81[ASN][1000 genomes]
rs17002829	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002831	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1813725	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1814033	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1847216	0.91[AMR][1000 genomes]
rs1980266	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2008222	0.84[ASN][1000 genomes]
rs2030463	0.98[ASN][1000 genomes]
rs2062637	0.82[ASN][1000 genomes]
rs2102116	1.00[ASN][1000 genomes]
rs2102190	0.81[AMR][1000 genomes]
rs2134048	0.90[ASN][1000 genomes]
rs2134459	0.91[AMR][1000 genomes]
rs2173869	0.95[ASN][1000 genomes]
rs2866444	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2866688	0.81[ASN][1000 genomes]
rs2866689	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866690	0.89[ASN][1000 genomes]
rs28796999	0.90[AMR][1000 genomes]
rs28891692	0.90[AMR][1000 genomes]
rs2903291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3205281	0.90[ASN][1000 genomes]
rs4078523	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4304001	0.81[ASN][1000 genomes]
rs4331798	0.85[AMR][1000 genomes]
rs4365752	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4410552	0.81[ASN][1000 genomes]
rs4417999	0.87[AMR][1000 genomes]
rs4472161	0.87[ASN][1000 genomes]
rs4473672	0.85[AMR][1000 genomes]
rs4541532	0.95[ASN][1000 genomes]
rs4859506	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859871	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859872	0.98[ASN][1000 genomes]
rs4859876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55694923	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55886549	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57221952	0.91[AMR][1000 genomes]
rs57246363	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57357866	0.82[ASN][1000 genomes]
rs57868780	0.87[AMR][1000 genomes]
rs58054752	0.91[AMR][1000 genomes]
rs58218398	0.90[AMR][1000 genomes]
rs6533217	0.88[ASN][1000 genomes]
rs6533226	0.93[ASN][1000 genomes]
rs6533239	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533269	0.95[ASN][1000 genomes]
rs6533270	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533271	0.95[ASN][1000 genomes]
rs6533272	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533274	0.92[ASN][1000 genomes]
rs6533290	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6533358	0.87[AMR][1000 genomes]
rs6533359	0.91[AMR][1000 genomes]
rs6533374	0.81[AMR][1000 genomes]
rs6533376	0.81[AMR][1000 genomes]
rs6814830	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6817305	0.81[ASN][1000 genomes]
rs6817823	0.95[ASN][1000 genomes]
rs6822317	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6823465	1.00[ASN][1000 genomes]
rs6828302	0.91[ASN][1000 genomes]
rs6830993	0.85[AMR][1000 genomes]
rs6833179	0.98[ASN][1000 genomes]
rs6839504	0.96[ASN][1000 genomes]
rs6849922	0.92[ASN][1000 genomes]
rs6850049	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6850111	1.00[ASN][1000 genomes]
rs6850590	0.91[AMR][1000 genomes]
rs6851286	0.81[AMR][1000 genomes]
rs6855336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857067	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6857479	0.81[AMR][1000 genomes]
rs72868269	0.81[ASN][1000 genomes]
rs73827437	0.80[ASN][1000 genomes]
rs73827443	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73827456	0.85[AMR][1000 genomes]
rs73827459	0.91[AMR][1000 genomes]
rs73827460	0.91[AMR][1000 genomes]
rs7655949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657658	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7674744	0.93[ASN][1000 genomes]
rs7686883	0.82[ASN][1000 genomes]
rs7693256	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs885376	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9991424	0.91[AMR][1000 genomes]
rs9993942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9996218	0.81[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	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv518757	chr4:78637265-78695138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7669988	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
2	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
3	chr4:78643800-78714000	Weak transcription	Lung	lung
4	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
6	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
7	chr4:78650200-78697800	Weak transcription	Gastric	stomach
8	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
11	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
13	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
14	chr4:78659800-78685800	Weak transcription	Psoas Muscle	Psoas
15	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
16	chr4:78662000-78695600	Weak transcription	Ovary	ovary
17	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
18	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
19	chr4:78662200-78682400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:78662800-78683400	Weak transcription	Fetal Kidney	kidney
22	chr4:78662800-78683600	Weak transcription	K562	blood
23	chr4:78663800-78695600	Weak transcription	Left Ventricle	heart
24	chr4:78665200-78682200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:78667200-78682600	Weak transcription	HepG2	liver
26	chr4:78673400-78682600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:78673400-78687000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:78673400-78692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:78673600-78682200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:78673600-78682400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:78673600-78682400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:78676200-78681800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr4:78676200-78682400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:78676200-78683400	Weak transcription	GM12878-XiMat	blood
35	chr4:78676200-78687400	Strong transcription	Fetal Thymus	thymus
36	chr4:78677400-78682400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:78677400-78682800	Strong transcription	Dnd41	blood
38	chr4:78677600-78682000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:78677600-78682400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr4:78677800-78682200	Weak transcription	Brain Anterior Caudate	brain
41	chr4:78677800-78682600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:78677800-78693800	Weak transcription	Hela-S3	cervix
43	chr4:78677800-78698400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:78678000-78682200	Weak transcription	Liver	Liver
45	chr4:78678000-78682400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:78678000-78682400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:78678000-78682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:78678000-78682400	Weak transcription	Adipose Nuclei	Adipose
49	chr4:78678000-78691200	Weak transcription	Placenta	Placenta
50	chr4:78678000-78691800	Weak transcription	HUVEC	blood vessel

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