Variant report

Variant	rs6823465
Chromosome Location	chr4:78676341-78676342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10005741	1.00[ASN][1000 genomes]
rs10007837	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1010728	0.86[AMR][1000 genomes]
rs10222901	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1039403	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10428319	0.82[AMR][1000 genomes]
rs10856982	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10856991	0.82[AMR][1000 genomes]
rs11097900	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11097935	0.95[ASN][1000 genomes]
rs11097965	0.88[AMR][1000 genomes]
rs1156059	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11727993	0.95[ASN][1000 genomes]
rs11730329	0.81[ASN][1000 genomes]
rs11730403	0.81[ASN][1000 genomes]
rs11731374	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11733759	0.80[ASN][1000 genomes]
rs11737353	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11939576	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12108312	0.86[AMR][1000 genomes]
rs12510593	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12643960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13105201	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13111592	1.00[ASN][1000 genomes]
rs13118459	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13128914	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13131896	0.81[ASN][1000 genomes]
rs13137909	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138341	0.88[ASN][1000 genomes]
rs13144225	0.95[ASN][1000 genomes]
rs13144226	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1402626	0.81[ASN][1000 genomes]
rs1501373	0.98[ASN][1000 genomes]
rs1521419	0.81[ASN][1000 genomes]
rs1554457	0.81[ASN][1000 genomes]
rs17002823	0.81[ASN][1000 genomes]
rs17002824	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002825	0.81[ASN][1000 genomes]
rs17002828	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17002829	0.81[ASN][1000 genomes]
rs17002831	0.81[ASN][1000 genomes]
rs1813725	0.93[ASN][1000 genomes]
rs1814033	0.84[ASN][1000 genomes]
rs1980266	0.81[ASN][1000 genomes]
rs2008222	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2030463	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2062637	0.82[ASN][1000 genomes]
rs2102116	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134048	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2173869	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2174078	0.86[AMR][1000 genomes]
rs2174080	0.86[AMR][1000 genomes]
rs2866444	0.91[ASN][1000 genomes]
rs2866688	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2866689	0.89[ASN][1000 genomes]
rs2866690	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2903291	0.95[ASN][1000 genomes]
rs3205281	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4304001	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4365752	0.81[ASN][1000 genomes]
rs4388114	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4410552	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4472161	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4541532	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4546268	0.82[AMR][1000 genomes]
rs4561950	0.82[AMR][1000 genomes]
rs4607246	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859506	0.93[ASN][1000 genomes]
rs4859871	0.88[ASN][1000 genomes]
rs4859872	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859876	1.00[ASN][1000 genomes]
rs4859878	0.95[ASN][1000 genomes]
rs55673370	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55694923	0.81[ASN][1000 genomes]
rs55886549	0.81[ASN][1000 genomes]
rs56138517	0.82[AMR][1000 genomes]
rs57246363	0.81[ASN][1000 genomes]
rs57357866	0.82[ASN][1000 genomes]
rs57501818	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57896992	0.86[AMR][1000 genomes]
rs58358199	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60135456	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6533217	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533226	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533239	0.98[ASN][1000 genomes]
rs6533269	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533270	0.95[ASN][1000 genomes]
rs6533271	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533272	0.95[ASN][1000 genomes]
rs6533274	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6533290	0.81[ASN][1000 genomes]
rs6814830	0.86[ASN][1000 genomes]
rs6817305	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6817823	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821826	0.86[AMR][1000 genomes]
rs6822317	0.81[ASN][1000 genomes]
rs6827822	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6828302	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6829203	0.94[EUR][1000 genomes]
rs6832015	0.82[AMR][1000 genomes]
rs6833179	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6836627	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6838630	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6839504	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6849922	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6850049	0.95[ASN][1000 genomes]
rs6850111	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854989	0.82[AMR][1000 genomes]
rs6855336	0.98[ASN][1000 genomes]
rs6857067	0.95[ASN][1000 genomes]
rs72868269	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72869573	0.84[AMR][1000 genomes]
rs73827437	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73827443	0.81[ASN][1000 genomes]
rs73827451	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7439347	0.82[AMR][1000 genomes]
rs7655949	1.00[ASN][1000 genomes]
rs7656319	0.86[AMR][1000 genomes]
rs7657658	0.81[ASN][1000 genomes]
rs7659122	0.82[AMR][1000 genomes]
rs7661064	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7663359	0.82[AMR][1000 genomes]
rs7669988	1.00[ASN][1000 genomes]
rs7671941	0.82[AMR][1000 genomes]
rs7673642	0.86[AMR][1000 genomes]
rs7674744	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7675586	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7686883	0.82[ASN][1000 genomes]
rs7687170	0.82[AMR][1000 genomes]
rs7687812	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7689226	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7692075	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7693256	0.91[ASN][1000 genomes]
rs885376	0.87[ASN][1000 genomes]
rs9993942	0.93[ASN][1000 genomes]
rs9996218	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6823465	CNOT6L	cis	Artery Tibial	GTEx
rs6823465	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs6823465	CNOT6L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
3	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
4	chr4:78643800-78714000	Weak transcription	Lung	lung
5	chr4:78645000-78676600	Weak transcription	Hela-S3	cervix
6	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:78646800-78677200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
9	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
10	chr4:78650200-78697800	Weak transcription	Gastric	stomach
11	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
14	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
16	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
17	chr4:78659000-78676600	Weak transcription	Fetal Stomach	stomach
18	chr4:78659800-78685800	Weak transcription	Psoas Muscle	Psoas
19	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
20	chr4:78662000-78695600	Weak transcription	Ovary	ovary
21	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
22	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
23	chr4:78662200-78682400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:78662600-78679800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:78662800-78676800	Weak transcription	Placenta	Placenta
27	chr4:78662800-78677600	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:78662800-78683400	Weak transcription	Fetal Kidney	kidney
29	chr4:78662800-78683600	Weak transcription	K562	blood
30	chr4:78663400-78677200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:78663600-78676800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:78663600-78676800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr4:78663800-78676800	Weak transcription	HSMM	muscle
34	chr4:78663800-78677200	Weak transcription	HUVEC	blood vessel
35	chr4:78663800-78678200	Weak transcription	HMEC	breast
36	chr4:78663800-78695600	Weak transcription	Left Ventricle	heart
37	chr4:78664600-78676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:78665200-78682200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:78667200-78682600	Weak transcription	HepG2	liver
40	chr4:78667400-78677200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:78672200-78676400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:78672400-78676600	Weak transcription	Fetal Lung	lung
43	chr4:78673000-78677200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:78673200-78678800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:78673200-78680000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:78673400-78676400	Weak transcription	Fetal Intestine Small	intestine
47	chr4:78673400-78676600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:78673400-78676600	Weak transcription	Adipose Nuclei	Adipose
49	chr4:78673400-78676800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:78673400-78676800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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