Variant report

Variant	rs4859506
Chromosome Location	chr4:78657220-78657221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:78657032-78657238	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:78647944..78650924-chr4:78655794..78657335,2	MCF-7	breast:
2	chr4:78649825..78652816-chr4:78654825..78657424,2	K562	blood:
3	chr4:78655466..78657702-chr4:78779436..78782397,2	K562	blood:

Variant related genes	Relation type
CNOT6L	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10005741	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10007837	0.93[ASN][1000 genomes]
rs10222901	0.88[ASN][1000 genomes]
rs1039403	0.96[ASN][1000 genomes]
rs1039467	0.91[AMR][1000 genomes]
rs10856982	0.88[ASN][1000 genomes]
rs11097935	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1156059	0.84[ASN][1000 genomes]
rs11721383	0.87[AMR][1000 genomes]
rs11723029	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11723221	0.90[AMR][1000 genomes]
rs11727993	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11729703	0.87[AMR][1000 genomes]
rs11730329	0.94[AMR][1000 genomes]
rs11730403	0.94[AMR][1000 genomes]
rs11732039	0.91[AMR][1000 genomes]
rs11733759	0.94[AMR][1000 genomes]
rs11734428	0.91[AMR][1000 genomes]
rs12510593	0.83[ASN][1000 genomes]
rs12643960	1.00[ASN][1000 genomes]
rs13105201	0.96[ASN][1000 genomes]
rs13111592	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13118459	0.93[ASN][1000 genomes]
rs13128914	0.96[ASN][1000 genomes]
rs13131896	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13137909	0.88[ASN][1000 genomes]
rs13138341	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13144225	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13144226	0.88[ASN][1000 genomes]
rs1402626	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1501373	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1521419	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1553386	0.91[AMR][1000 genomes]
rs1554457	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17002823	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17002825	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002829	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002831	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1813725	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1814033	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1847216	0.91[AMR][1000 genomes]
rs1980266	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2030463	0.90[ASN][1000 genomes]
rs2102116	0.93[ASN][1000 genomes]
rs2134048	0.98[ASN][1000 genomes]
rs2134459	0.91[AMR][1000 genomes]
rs2173869	0.88[ASN][1000 genomes]
rs2866444	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2866689	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2866690	0.96[ASN][1000 genomes]
rs28796999	0.90[AMR][1000 genomes]
rs28891692	0.90[AMR][1000 genomes]
rs2903291	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3205281	0.98[ASN][1000 genomes]
rs4078523	0.94[AMR][1000 genomes]
rs4331798	0.85[AMR][1000 genomes]
rs4365752	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4417999	0.87[AMR][1000 genomes]
rs4472161	0.94[ASN][1000 genomes]
rs4473672	0.85[AMR][1000 genomes]
rs4541532	0.88[ASN][1000 genomes]
rs4859871	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859872	0.95[ASN][1000 genomes]
rs4859876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859878	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55694923	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55886549	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57221952	0.91[AMR][1000 genomes]
rs57246363	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57868780	0.87[AMR][1000 genomes]
rs58054752	0.91[AMR][1000 genomes]
rs58218398	0.90[AMR][1000 genomes]
rs6533217	0.95[ASN][1000 genomes]
rs6533226	1.00[ASN][1000 genomes]
rs6533239	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533269	0.88[ASN][1000 genomes]
rs6533270	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533271	0.88[ASN][1000 genomes]
rs6533272	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533274	0.85[ASN][1000 genomes]
rs6533290	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs6533358	0.87[AMR][1000 genomes]
rs6533359	0.91[AMR][1000 genomes]
rs6814830	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6817823	0.88[ASN][1000 genomes]
rs6822317	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6823465	0.93[ASN][1000 genomes]
rs6828302	0.84[ASN][1000 genomes]
rs6830993	0.85[AMR][1000 genomes]
rs6833179	0.95[ASN][1000 genomes]
rs6839504	0.94[ASN][1000 genomes]
rs6849922	0.85[ASN][1000 genomes]
rs6850049	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850111	0.93[ASN][1000 genomes]
rs6850590	0.91[AMR][1000 genomes]
rs6855336	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6857067	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73827443	0.84[AMR][1000 genomes]
rs73827456	0.85[AMR][1000 genomes]
rs73827459	0.91[AMR][1000 genomes]
rs73827460	0.91[AMR][1000 genomes]
rs7655949	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7657658	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7669988	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674744	1.00[ASN][1000 genomes]
rs7693256	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs885376	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9991424	0.91[AMR][1000 genomes]
rs9993942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4859506	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:78630200-78660000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
4	chr4:78636400-78659000	Weak transcription	Psoas Muscle	Psoas
5	chr4:78637400-78661200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:78637400-78673200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:78639200-78661200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:78639400-78671200	Weak transcription	Brain Germinal Matrix	brain
9	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
10	chr4:78641000-78665000	Weak transcription	Fetal Brain Male	brain
11	chr4:78643800-78714000	Weak transcription	Lung	lung
12	chr4:78644800-78666600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:78645000-78664000	Weak transcription	A549	lung
14	chr4:78645000-78676600	Weak transcription	Hela-S3	cervix
15	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:78645600-78663200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:78645800-78658800	Weak transcription	Fetal Stomach	stomach
18	chr4:78646000-78664000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:78646200-78663800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:78646800-78677200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:78649800-78660800	Weak transcription	HSMM	muscle
22	chr4:78650000-78659200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:78650000-78660200	Weak transcription	Brain Anterior Caudate	brain
24	chr4:78650000-78663200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
26	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
27	chr4:78650200-78659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:78650200-78659000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:78650200-78659200	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:78650200-78660400	Weak transcription	HMEC	breast
31	chr4:78650200-78661200	Weak transcription	Aorta	Aorta
32	chr4:78650200-78661200	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:78650200-78661200	Weak transcription	Left Ventricle	heart
34	chr4:78650200-78661200	Weak transcription	Ovary	ovary
35	chr4:78650200-78661200	Weak transcription	Pancreas	Pancrea
36	chr4:78650200-78661800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:78650200-78662600	Weak transcription	Right Ventricle	heart
38	chr4:78650200-78663800	Weak transcription	Fetal Brain Female	brain
39	chr4:78650200-78673000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:78650200-78673000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr4:78650200-78697800	Weak transcription	Gastric	stomach
42	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
45	chr4:78650400-78659200	Weak transcription	Fetal Kidney	kidney
46	chr4:78650400-78660800	Weak transcription	Brain Angular Gyrus	brain
47	chr4:78650600-78658800	Weak transcription	Fetal Lung	lung
48	chr4:78650600-78659200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:78650600-78659200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:78650600-78665800	Weak transcription	Fetal Muscle Leg	muscle

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