Variant report

Variant	rs13144225
Chromosome Location	chr4:78717276-78717277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78715797..78717361-chr9:125546307..125548582,2	MCF-7	breast:
2	chr4:78714906..78717368-chr4:78741847..78743752,2	K562	blood:

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10005741	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10007837	0.95[ASN][1000 genomes]
rs10222901	1.00[ASN][1000 genomes]
rs1039403	0.85[ASN][1000 genomes]
rs1039467	0.91[AMR][1000 genomes]
rs10856982	1.00[ASN][1000 genomes]
rs11097935	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156059	0.95[ASN][1000 genomes]
rs11721383	0.87[AMR][1000 genomes]
rs11723029	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11723221	0.90[AMR][1000 genomes]
rs11727993	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729703	0.87[AMR][1000 genomes]
rs11730329	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11730403	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11732039	0.91[AMR][1000 genomes]
rs11733759	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11734428	0.91[AMR][1000 genomes]
rs11939576	0.86[ASN][1000 genomes]
rs12510593	0.81[ASN][1000 genomes]
rs12643960	0.88[ASN][1000 genomes]
rs13105201	0.85[ASN][1000 genomes]
rs13111592	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118459	0.95[ASN][1000 genomes]
rs13128914	0.85[ASN][1000 genomes]
rs13131896	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13137909	1.00[ASN][1000 genomes]
rs13138341	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13144226	1.00[ASN][1000 genomes]
rs1402626	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1501373	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1502880	0.81[AMR][1000 genomes]
rs1521419	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1553386	0.91[AMR][1000 genomes]
rs1554457	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17002823	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17002824	0.86[ASN][1000 genomes]
rs17002825	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17002828	0.86[ASN][1000 genomes]
rs17002829	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17002831	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1813725	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814033	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1847216	0.91[AMR][1000 genomes]
rs1980266	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2008222	0.88[ASN][1000 genomes]
rs2030463	0.98[ASN][1000 genomes]
rs2102116	0.95[ASN][1000 genomes]
rs2102190	0.81[AMR][1000 genomes]
rs2134048	0.86[ASN][1000 genomes]
rs2134459	0.91[AMR][1000 genomes]
rs2173869	1.00[ASN][1000 genomes]
rs2866444	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866688	0.86[ASN][1000 genomes]
rs2866689	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2866690	0.85[ASN][1000 genomes]
rs28796999	0.90[AMR][1000 genomes]
rs28891692	0.90[AMR][1000 genomes]
rs2903291	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3205281	0.86[ASN][1000 genomes]
rs4078523	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4304001	0.86[ASN][1000 genomes]
rs4331798	0.85[AMR][1000 genomes]
rs4365752	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4410552	0.86[ASN][1000 genomes]
rs4417999	0.87[AMR][1000 genomes]
rs4472161	0.83[ASN][1000 genomes]
rs4473672	0.85[AMR][1000 genomes]
rs4541532	1.00[ASN][1000 genomes]
rs4859506	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859871	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859872	0.93[ASN][1000 genomes]
rs4859876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55694923	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55886549	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57221952	0.91[AMR][1000 genomes]
rs57246363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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];0.81[ASN][1000 genomes]
rs60135456	0.84[ASN][1000 genomes]
rs6533217	0.84[ASN][1000 genomes]
rs6533226	0.88[ASN][1000 genomes]
rs6533239	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533269	1.00[ASN][1000 genomes]
rs6533270	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533271	1.00[ASN][1000 genomes]
rs6533272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533274	0.96[ASN][1000 genomes]
rs6533290	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[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	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6817305	0.86[ASN][1000 genomes]
rs6817823	1.00[ASN][1000 genomes]
rs6822317	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6823465	0.95[ASN][1000 genomes]
rs6827822	0.84[ASN][1000 genomes]
rs6828302	0.95[ASN][1000 genomes]
rs6829203	0.83[ASN][1000 genomes]
rs6830993	0.85[AMR][1000 genomes]
rs6833179	0.93[ASN][1000 genomes]
rs6839504	0.92[ASN][1000 genomes]
rs6849922	0.96[ASN][1000 genomes]
rs6850049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850111	0.95[ASN][1000 genomes]
rs6850590	0.91[AMR][1000 genomes]
rs6851286	0.81[AMR][1000 genomes]
rs6855336	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6857067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857479	0.81[AMR][1000 genomes]
rs72868269	0.86[ASN][1000 genomes]
rs73827437	0.85[ASN][1000 genomes]
rs73827443	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73827456	0.85[AMR][1000 genomes]
rs73827459	0.91[AMR][1000 genomes]
rs73827460	0.91[AMR][1000 genomes]
rs7655949	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7657658	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7669988	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674744	0.88[ASN][1000 genomes]
rs7686883	0.86[ASN][1000 genomes]
rs7693256	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs885376	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9991424	0.91[AMR][1000 genomes]
rs9993942	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9996218	0.86[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	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
3	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
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13144225	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
2	chr4:78694200-78722000	Weak transcription	Fetal Stomach	stomach
3	chr4:78696400-78717600	Weak transcription	Thymus	Thymus
4	chr4:78697400-78721400	Weak transcription	Placenta	Placenta
5	chr4:78698600-78717400	Weak transcription	Right Ventricle	heart
6	chr4:78698600-78720200	Weak transcription	Dnd41	blood
7	chr4:78698800-78717400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:78701600-78721400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:78703600-78718000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:78704800-78722200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:78705800-78720000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:78706000-78717600	Weak transcription	Right Atrium	heart
13	chr4:78706200-78719800	Weak transcription	Fetal Intestine Small	intestine
14	chr4:78707400-78720200	Weak transcription	Gastric	stomach
15	chr4:78707600-78717800	Weak transcription	Esophagus	oesophagus
16	chr4:78709200-78721400	Weak transcription	Brain Substantia Nigra	brain
17	chr4:78710200-78722000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:78711000-78717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:78711000-78718000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:78711000-78722200	Weak transcription	Ovary	ovary
21	chr4:78711400-78722000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:78711600-78721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:78711600-78722200	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:78711800-78721800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:78712000-78718000	Weak transcription	NHEK	skin
26	chr4:78712800-78722000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:78713600-78721600	Weak transcription	HUVEC	blood vessel
28	chr4:78714200-78720200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:78714200-78721200	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:78714200-78721600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:78714800-78717600	Weak transcription	Pancreas	Pancrea
32	chr4:78714800-78719000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:78714800-78721400	Weak transcription	Small Intestine	intestine
34	chr4:78715000-78720000	Weak transcription	Psoas Muscle	Psoas
35	chr4:78715400-78717600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:78715400-78718000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:78716400-78717800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:78716400-78718000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
39	chr4:78716400-78718000	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr4:78716400-78718200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:78716400-78722000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:78716400-78733400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr4:78716600-78717600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr4:78716600-78717600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:78716600-78717800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
46	chr4:78716600-78718200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr4:78716600-78718200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:78716600-78718800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:78716600-78722000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr4:78716800-78717400	Weak transcription	Primary T cells from cord blood	blood

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