Variant report

Variant	rs6833179
Chromosome Location	chr4:78664838-78664839
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	CTCF	chr4:78664821-78664904	GM10248	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78664695..78666373-chr4:78741463..78744231,2	K562	blood:
2	chr4:78660857..78662460-chr4:78663917..78665509,2	K562	blood:

Variant related genes	Relation type
CNOT6L	TF binding region

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10005741	0.98[ASN][1000 genomes]
rs10007837	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];0.93[ASN][1000 genomes]
rs1039403	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10428319	0.82[AMR][1000 genomes]
rs10856982	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10856991	0.82[AMR][1000 genomes]
rs11097900	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11097935	0.93[ASN][1000 genomes]
rs11097965	0.88[AMR][1000 genomes]
rs1156059	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11727993	0.93[ASN][1000 genomes]
rs11731374	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11737353	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11939576	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12108312	0.86[AMR][1000 genomes]
rs12510593	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12643960	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13105201	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13111592	0.98[ASN][1000 genomes]
rs13118459	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128914	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13137909	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13138341	0.90[ASN][1000 genomes]
rs13144225	0.93[ASN][1000 genomes]
rs13144226	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1501373	0.95[ASN][1000 genomes]
rs17002824	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17002828	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1813725	0.90[ASN][1000 genomes]
rs1814033	0.82[ASN][1000 genomes]
rs2008222	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2030463	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2062637	0.85[ASN][1000 genomes]
rs2102116	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134048	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2173869	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2174078	0.86[AMR][1000 genomes]
rs2174080	0.86[AMR][1000 genomes]
rs2866444	0.89[ASN][1000 genomes]
rs2866688	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2866689	0.92[ASN][1000 genomes]
rs2866690	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2903291	0.93[ASN][1000 genomes]
rs3205281	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4304001	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4388114	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4410552	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4472161	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4541532	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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	0.95[ASN][1000 genomes]
rs4859871	0.90[ASN][1000 genomes]
rs4859872	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859876	0.98[ASN][1000 genomes]
rs4859878	0.93[ASN][1000 genomes]
rs55673370	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56138517	0.82[AMR][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	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533226	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533239	1.00[ASN][1000 genomes]
rs6533269	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533270	0.93[ASN][1000 genomes]
rs6533271	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533272	0.93[ASN][1000 genomes]
rs6533274	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6814830	0.84[ASN][1000 genomes]
rs6817305	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6817823	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6821826	0.86[AMR][1000 genomes]
rs6823465	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827822	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6828302	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829203	0.94[EUR][1000 genomes]
rs6832015	0.82[AMR][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	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849922	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6850049	0.93[ASN][1000 genomes]
rs6850111	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6854989	0.82[AMR][1000 genomes]
rs6855336	1.00[ASN][1000 genomes]
rs6857067	0.93[ASN][1000 genomes]
rs72868269	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72869573	0.84[AMR][1000 genomes]
rs73827437	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73827451	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7439347	0.82[AMR][1000 genomes]
rs7655949	0.98[ASN][1000 genomes]
rs7656319	0.86[AMR][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	0.98[ASN][1000 genomes]
rs7671941	0.82[AMR][1000 genomes]
rs7673642	0.86[AMR][1000 genomes]
rs7674744	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7675586	0.88[AMR][1000 genomes];0.80[EUR][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	0.89[ASN][1000 genomes]
rs885376	0.89[ASN][1000 genomes]
rs9993942	0.95[ASN][1000 genomes]
rs9996218	0.98[AMR][1000 genomes];0.93[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6833179	CNOT6L	cis	Artery Tibial	GTEx
rs6833179	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 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	chr4:78637400-78673200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:78639400-78671200	Weak transcription	Brain Germinal Matrix	brain
5	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
6	chr4:78641000-78665000	Weak transcription	Fetal Brain Male	brain
7	chr4:78643800-78714000	Weak transcription	Lung	lung
8	chr4:78644800-78666600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:78645000-78676600	Weak transcription	Hela-S3	cervix
10	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:78646800-78677200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
13	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
14	chr4:78650200-78673000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:78650200-78673000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:78650200-78697800	Weak transcription	Gastric	stomach
17	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
20	chr4:78650600-78665800	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:78650800-78697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:78653200-78673200	Weak transcription	Fetal Heart	heart
23	chr4:78654200-78697600	Weak transcription	HSMMtube	muscle
24	chr4:78656600-78667800	Strong transcription	Fetal Thymus	thymus
25	chr4:78657000-78695600	Weak transcription	Small Intestine	intestine
26	chr4:78657400-78673000	Weak transcription	Fetal Intestine Small	intestine
27	chr4:78658600-78669400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:78659000-78676600	Weak transcription	Fetal Stomach	stomach
29	chr4:78659200-78673000	Strong transcription	Primary B cells from cord blood	blood
30	chr4:78659600-78671400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:78659600-78672000	Weak transcription	GM12878-XiMat	blood
32	chr4:78659600-78673000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:78659800-78676000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:78659800-78685800	Weak transcription	Psoas Muscle	Psoas
35	chr4:78659800-78697800	Weak transcription	Esophagus	oesophagus
36	chr4:78660200-78667800	Weak transcription	NHLF	lung
37	chr4:78662000-78666600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:78662000-78695600	Weak transcription	Ovary	ovary
39	chr4:78662000-78697600	Weak transcription	Brain Angular Gyrus	brain
40	chr4:78662000-78697800	Weak transcription	Pancreas	Pancrea
41	chr4:78662200-78668600	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:78662200-78682400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:78662200-78697800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:78662400-78673000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:78662600-78672400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:78662600-78679800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:78662800-78665800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:78662800-78667000	Weak transcription	HepG2	liver
49	chr4:78662800-78671200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:78662800-78672000	Weak transcription	Fetal Lung	lung

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