Variant report

Variant	rs58054752
Chromosome Location	chr4:78846344-78846345
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	chr4:78830111..78832378-chr4:78846215..78847965,2	MCF-7	breast:

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10005741	0.88[AMR][1000 genomes]
rs1010728	0.96[ASN][1000 genomes]
rs1039467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10428319	1.00[ASN][1000 genomes]
rs10856991	0.85[ASN][1000 genomes]
rs11097935	0.91[AMR][1000 genomes]
rs11097965	0.90[ASN][1000 genomes]
rs11097980	0.82[AMR][1000 genomes]
rs11721383	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11723221	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11727993	0.91[AMR][1000 genomes]
rs11729703	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730329	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11730403	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11732039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733759	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11734428	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11937191	0.84[EUR][1000 genomes]
rs12108312	0.98[ASN][1000 genomes]
rs12507708	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12650649	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13111592	0.88[AMR][1000 genomes]
rs13131896	0.91[AMR][1000 genomes]
rs13138341	0.84[AMR][1000 genomes]
rs13144225	0.91[AMR][1000 genomes]
rs1402626	0.85[AMR][1000 genomes]
rs1501373	0.91[AMR][1000 genomes]
rs1502879	0.80[ASN][1000 genomes]
rs1502880	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1521419	0.91[AMR][1000 genomes]
rs1553386	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554457	0.91[AMR][1000 genomes]
rs17002823	0.91[AMR][1000 genomes]
rs17002825	0.91[AMR][1000 genomes]
rs17002829	0.85[AMR][1000 genomes]
rs17002831	0.85[AMR][1000 genomes]
rs1814033	0.91[AMR][1000 genomes]
rs1847215	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1847216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1910304	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1980266	0.91[AMR][1000 genomes]
rs2036458	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2102190	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2134459	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2174078	0.91[ASN][1000 genomes]
rs2174080	0.91[ASN][1000 genomes]
rs2866689	0.88[AMR][1000 genomes]
rs28796999	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28891692	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2903291	0.91[AMR][1000 genomes]
rs35896758	0.81[EUR][1000 genomes]
rs3860617	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4078523	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4331798	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365752	0.91[AMR][1000 genomes]
rs4388114	0.82[ASN][1000 genomes]
rs4417999	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4473672	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546268	0.96[ASN][1000 genomes]
rs4561950	1.00[ASN][1000 genomes]
rs4607246	0.82[ASN][1000 genomes]
rs4859506	0.91[AMR][1000 genomes]
rs4859871	0.84[AMR][1000 genomes]
rs4859876	0.91[AMR][1000 genomes]
rs4859878	0.91[AMR][1000 genomes]
rs4859898	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859899	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859900	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859901	0.80[ASN][1000 genomes]
rs55694923	0.85[AMR][1000 genomes]
rs55886549	0.91[AMR][1000 genomes]
rs56138517	0.96[ASN][1000 genomes]
rs57221952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57246363	0.91[AMR][1000 genomes]
rs57868780	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57896992	1.00[ASN][1000 genomes]
rs58218398	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533239	0.88[AMR][1000 genomes]
rs6533270	0.91[AMR][1000 genomes]
rs6533272	0.91[AMR][1000 genomes]
rs6533290	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533358	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533359	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533374	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6533376	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6533382	0.80[ASN][1000 genomes]
rs6821826	1.00[ASN][1000 genomes]
rs6822317	0.91[AMR][1000 genomes]
rs6830993	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832015	0.96[ASN][1000 genomes]
rs6850049	0.91[AMR][1000 genomes]
rs6850590	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6851286	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6854989	0.96[ASN][1000 genomes]
rs6855336	0.91[AMR][1000 genomes]
rs6857067	0.91[AMR][1000 genomes]
rs6857479	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72869573	0.95[ASN][1000 genomes]
rs73827443	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73827451	0.82[ASN][1000 genomes]
rs73827456	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73827459	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73827460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7439347	1.00[ASN][1000 genomes]
rs7655949	0.91[AMR][1000 genomes]
rs7656319	0.98[ASN][1000 genomes]
rs7657658	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7659122	0.98[ASN][1000 genomes]
rs7663359	0.96[ASN][1000 genomes]
rs7669988	0.91[AMR][1000 genomes]
rs7671941	0.95[ASN][1000 genomes]
rs7673642	0.98[ASN][1000 genomes]
rs7687170	0.96[ASN][1000 genomes]
rs7693256	0.82[AMR][1000 genomes]
rs7699987	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs885376	0.84[AMR][1000 genomes]
rs9991424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9993942	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv3327080	chr4:78845375-78846442	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58054752	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
2	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
3	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
4	chr4:78794200-78851800	Weak transcription	Lung	lung
5	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
6	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
8	chr4:78808800-78852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:78809200-78847000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:78809600-78851200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:78809600-78851400	Weak transcription	Ovary	ovary
12	chr4:78809600-78865400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:78810000-78851800	Weak transcription	Thymus	Thymus
15	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea
16	chr4:78816400-78866400	Weak transcription	Fetal Thymus	thymus
17	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:78816600-78851400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:78816600-78875800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:78818800-78872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:78819200-78852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:78819600-78851200	Weak transcription	Adipose Nuclei	Adipose
23	chr4:78820800-78851200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:78821000-78849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:78821000-78866000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:78821400-78873200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:78830000-78866600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:78830200-78846400	Weak transcription	Fetal Intestine Small	intestine
29	chr4:78830200-78847200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:78830200-78851200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:78830200-78852000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:78831800-78865800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:78832000-78846800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:78832000-78851400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:78832000-78858000	Weak transcription	Fetal Stomach	stomach
37	chr4:78833400-78846600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr4:78833400-78847200	Weak transcription	K562	blood
39	chr4:78833400-78851400	Weak transcription	Liver	Liver
40	chr4:78833600-78865400	Weak transcription	Fetal Kidney	kidney
41	chr4:78834000-78852800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:78834800-78847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:78835400-78847200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr4:78835400-78852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:78838600-78851000	Weak transcription	GM12878-XiMat	blood
46	chr4:78840800-78849200	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:78842200-78846400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:78842200-78865600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr4:78842400-78865400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:78842800-78851600	Weak transcription	HSMMtube	muscle

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