Variant report

Variant	rs57868780
Chromosome Location	chr4:78797333-78797334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78782527..78785375-chr4:78792236..78798548,6	MCF-7	breast:
2	chr4:78786547..78788323-chr4:78797006..78799042,2	K562	blood:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10005741	0.85[AMR][1000 genomes]
rs1039467	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11097935	0.87[AMR][1000 genomes]
rs11097965	0.85[ASN][1000 genomes]
rs11721383	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11723221	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11727993	0.87[AMR][1000 genomes]
rs11729703	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11730329	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11730403	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11731374	1.00[ASN][1000 genomes]
rs11732039	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11733759	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11734428	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11737353	1.00[ASN][1000 genomes]
rs11737861	0.81[ASN][1000 genomes]
rs11939576	0.90[ASN][1000 genomes]
rs13111592	0.85[AMR][1000 genomes]
rs13131896	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13138341	0.81[AMR][1000 genomes]
rs13144225	0.87[AMR][1000 genomes]
rs1402626	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1501373	0.87[AMR][1000 genomes]
rs1521419	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1553386	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1554457	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17002823	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17002824	0.90[ASN][1000 genomes]
rs17002825	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17002828	0.90[ASN][1000 genomes]
rs17002829	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17002831	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1814033	0.87[AMR][1000 genomes]
rs1847216	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1980266	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2134459	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2866688	0.90[ASN][1000 genomes]
rs2866689	0.84[AMR][1000 genomes]
rs28796999	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28891692	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2903291	0.87[AMR][1000 genomes]
rs4078523	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4304001	0.90[ASN][1000 genomes]
rs4331798	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4365752	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4388114	0.93[ASN][1000 genomes]
rs4410552	0.90[ASN][1000 genomes]
rs4417999	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4473672	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4546268	0.80[ASN][1000 genomes]
rs4607246	0.93[ASN][1000 genomes]
rs4859506	0.87[AMR][1000 genomes]
rs4859871	0.81[AMR][1000 genomes]
rs4859876	0.87[AMR][1000 genomes]
rs4859878	0.87[AMR][1000 genomes]
rs55673370	1.00[ASN][1000 genomes]
rs55694923	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55886549	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56138517	0.80[ASN][1000 genomes]
rs57221952	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57246363	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57501818	0.98[ASN][1000 genomes]
rs58054752	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58218398	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58358199	0.97[ASN][1000 genomes]
rs60135456	0.92[ASN][1000 genomes]
rs6533239	0.85[AMR][1000 genomes]
rs6533270	0.87[AMR][1000 genomes]
rs6533272	0.87[AMR][1000 genomes]
rs6533290	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533358	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533359	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6817305	0.90[ASN][1000 genomes]
rs6822317	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6827822	0.92[ASN][1000 genomes]
rs6830993	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6832015	0.80[ASN][1000 genomes]
rs6836627	0.98[ASN][1000 genomes]
rs6838630	0.98[ASN][1000 genomes]
rs6850049	0.87[AMR][1000 genomes]
rs6850590	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6854989	0.80[ASN][1000 genomes]
rs6855336	0.87[AMR][1000 genomes]
rs6857067	0.87[AMR][1000 genomes]
rs72868269	0.90[ASN][1000 genomes]
rs72869573	0.81[ASN][1000 genomes]
rs73827437	0.89[ASN][1000 genomes]
rs73827443	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73827451	0.93[ASN][1000 genomes]
rs73827456	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73827459	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73827460	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7655949	0.87[AMR][1000 genomes]
rs7657658	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7661064	0.98[ASN][1000 genomes]
rs7663359	0.80[ASN][1000 genomes]
rs7669988	0.87[AMR][1000 genomes]
rs7671941	0.81[ASN][1000 genomes]
rs7675586	0.95[ASN][1000 genomes]
rs7687170	0.80[ASN][1000 genomes]
rs7687812	0.98[ASN][1000 genomes]
rs7689226	0.99[ASN][1000 genomes]
rs7692075	0.97[ASN][1000 genomes]
rs885376	0.81[AMR][1000 genomes]
rs9991424	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9993942	0.87[AMR][1000 genomes]
rs9996218	0.90[ASN][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	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs57868780	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784600-78801800	Weak transcription	Aorta	Aorta
2	chr4:78784800-78808400	Weak transcription	Brain Substantia Nigra	brain
3	chr4:78784800-78842200	Weak transcription	HSMMtube	muscle
4	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
5	chr4:78785000-78798400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:78785000-78798800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:78785000-78798800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:78785000-78801400	Weak transcription	Pancreas	Pancrea
9	chr4:78785000-78801400	Weak transcription	Psoas Muscle	Psoas
10	chr4:78785000-78803000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:78785000-78805800	Weak transcription	Colonic Mucosa	Colon
12	chr4:78785000-78807000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:78785000-78808400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:78785000-78808800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:78785000-78810600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
17	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
20	chr4:78785200-78798800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:78785200-78805000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:78785200-78806600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:78785200-78808400	Weak transcription	Fetal Brain Male	brain
24	chr4:78785200-78816200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr4:78785200-78818800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:78785200-78820800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:78785400-78798800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:78785400-78808200	Weak transcription	Fetal Kidney	kidney
29	chr4:78785400-78829800	Weak transcription	Fetal Heart	heart
30	chr4:78785600-78808200	Weak transcription	Hela-S3	cervix
31	chr4:78785600-78808400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:78786000-78803000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:78786000-78804000	Weak transcription	Fetal Intestine Large	intestine
34	chr4:78786600-78799800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:78787200-78801400	Weak transcription	A549	lung
36	chr4:78790400-78808200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:78790400-78808400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr4:78790600-78843400	Weak transcription	Small Intestine	intestine
39	chr4:78790800-78817400	Weak transcription	NH-A	brain
40	chr4:78791400-78808000	Weak transcription	Ovary	ovary
41	chr4:78792200-78797400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:78792400-78800400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:78792400-78802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:78792600-78804000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr4:78793000-78797400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:78793000-78797400	Strong transcription	Fetal Thymus	thymus
47	chr4:78793000-78797800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:78793000-78800200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:78793200-78797400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:78793200-78797400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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