Variant report

Variant	rs57896992
Chromosome Location	chr4:78846496-78846497
allele	G/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: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10007837	0.88[AMR][1000 genomes]
rs1010728	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10222901	0.88[AMR][1000 genomes]
rs1039403	0.86[AMR][1000 genomes]
rs1039467	0.98[ASN][1000 genomes]
rs10428319	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10856982	0.88[AMR][1000 genomes]
rs10856991	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11097900	0.82[AMR][1000 genomes]
rs11097965	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1156059	0.88[AMR][1000 genomes]
rs11721383	0.90[ASN][1000 genomes]
rs11723221	0.84[ASN][1000 genomes]
rs11729703	0.95[ASN][1000 genomes]
rs11731374	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11732039	1.00[ASN][1000 genomes]
rs11734428	0.98[ASN][1000 genomes]
rs11737353	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11939576	0.88[AMR][1000 genomes]
rs12108312	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12507708	0.80[ASN][1000 genomes]
rs12643960	0.86[AMR][1000 genomes]
rs13105201	0.86[AMR][1000 genomes]
rs13118459	0.88[AMR][1000 genomes]
rs13128914	0.84[AMR][1000 genomes]
rs13137909	0.88[AMR][1000 genomes]
rs13144226	0.88[AMR][1000 genomes]
rs1502879	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1502880	0.80[ASN][1000 genomes]
rs1553386	0.86[ASN][1000 genomes]
rs17002824	0.88[AMR][1000 genomes]
rs17002828	0.84[AMR][1000 genomes]
rs1847216	0.98[ASN][1000 genomes]
rs2030463	0.88[AMR][1000 genomes]
rs2036458	0.80[ASN][1000 genomes]
rs2102116	0.86[AMR][1000 genomes]
rs2134048	0.84[AMR][1000 genomes]
rs2134459	0.93[ASN][1000 genomes]
rs2173869	0.88[AMR][1000 genomes]
rs2174078	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2174079	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2174080	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2866688	0.88[AMR][1000 genomes]
rs2866690	0.84[AMR][1000 genomes]
rs3205281	0.86[AMR][1000 genomes]
rs3860617	0.94[ASN][1000 genomes]
rs4304001	0.84[AMR][1000 genomes]
rs4331798	1.00[ASN][1000 genomes]
rs4388114	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4410552	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4417999	0.95[ASN][1000 genomes]
rs4472161	0.84[AMR][1000 genomes]
rs4473672	1.00[ASN][1000 genomes]
rs4541532	0.88[AMR][1000 genomes]
rs4546268	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4561950	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607246	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859515	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859872	0.88[AMR][1000 genomes]
rs4859894	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859896	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859897	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859899	0.80[ASN][1000 genomes]
rs4859900	0.80[ASN][1000 genomes]
rs4859901	0.80[ASN][1000 genomes]
rs55673370	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56138517	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57221952	1.00[ASN][1000 genomes]
rs57501818	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58054752	1.00[ASN][1000 genomes]
rs58358199	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60135456	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533217	0.86[AMR][1000 genomes]
rs6533226	0.84[AMR][1000 genomes]
rs6533269	0.88[AMR][1000 genomes]
rs6533271	0.88[AMR][1000 genomes]
rs6533274	0.86[AMR][1000 genomes]
rs6533358	0.90[ASN][1000 genomes]
rs6533359	0.90[ASN][1000 genomes]
rs6533374	0.80[ASN][1000 genomes]
rs6533376	0.80[ASN][1000 genomes]
rs6533382	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6817305	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6817823	0.88[AMR][1000 genomes]
rs6821826	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823465	0.86[AMR][1000 genomes]
rs6827822	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6828302	0.88[AMR][1000 genomes]
rs6830993	0.96[ASN][1000 genomes]
rs6832015	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6833179	0.86[AMR][1000 genomes]
rs6836627	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6838630	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6839504	0.88[AMR][1000 genomes]
rs6849922	0.88[AMR][1000 genomes]
rs6850111	0.88[AMR][1000 genomes]
rs6850590	0.90[ASN][1000 genomes]
rs6851286	0.80[ASN][1000 genomes]
rs6854989	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857479	0.80[ASN][1000 genomes]
rs72868269	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72869573	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73827437	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73827451	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73827456	0.90[ASN][1000 genomes]
rs73827459	0.98[ASN][1000 genomes]
rs73827460	0.98[ASN][1000 genomes]
rs7439347	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656319	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7659122	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661064	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7663359	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7671432	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7671941	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673642	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7674744	0.88[AMR][1000 genomes]
rs7675586	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7687170	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687812	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7689226	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7692075	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs950263	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs950264	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9991424	0.88[ASN][1000 genomes]
rs9996218	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57896992	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	chr4:78830200-78847200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:78830200-78851200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:78830200-78852000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:78831800-78865800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:78832000-78846800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:78832000-78851400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:78832000-78858000	Weak transcription	Fetal Stomach	stomach
36	chr4:78833400-78846600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:78833400-78847200	Weak transcription	K562	blood
38	chr4:78833400-78851400	Weak transcription	Liver	Liver
39	chr4:78833600-78865400	Weak transcription	Fetal Kidney	kidney
40	chr4:78834000-78852800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:78834800-78847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:78835400-78847200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:78835400-78852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:78838600-78851000	Weak transcription	GM12878-XiMat	blood
45	chr4:78840800-78849200	Weak transcription	Colon Smooth Muscle	Colon
46	chr4:78842200-78865600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:78842400-78865400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:78842800-78851600	Weak transcription	HSMMtube	muscle
49	chr4:78843200-78846800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:78843400-78847200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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