Variant report

Variant	rs6829203
Chromosome Location	chr4:78739891-78739892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78739575..78742806-chr4:78977392..78979889,3	MCF-7	breast:
2	chr4:78739289..78742998-chr4:78782109..78787360,12	MCF-7	breast:
3	chr4:78739409..78741307-chr4:83294294..83296166,2	MCF-7	breast:
4	chr4:78739575..78741919-chr4:78878334..78880056,2	MCF-7	breast:
5	chr4:78738764..78744926-chr4:78780904..78785516,9	MCF-7	breast:
6	chr4:78734703..78743448-chr4:78779372..78785561,20	K562	blood:
7	chr4:78738995..78744410-chr4:78782336..78785612,12	K562	blood:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction
ENSG00000248926	Chromatin interaction
ENSG00000138668	Chromatin interaction
ENSG00000138759	Chromatin interaction
ENSG00000250214	Chromatin interaction
ENSG00000272677	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10007837	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10222901	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1039403	0.94[EUR][1000 genomes]
rs10856982	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097900	0.84[EUR][1000 genomes]
rs11097935	0.83[ASN][1000 genomes]
rs1156059	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11727993	0.83[ASN][1000 genomes]
rs11731374	0.84[EUR][1000 genomes]
rs11737353	0.84[EUR][1000 genomes]
rs11939576	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12643960	0.94[EUR][1000 genomes]
rs13105201	0.94[EUR][1000 genomes]
rs13118459	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13128914	0.93[EUR][1000 genomes]
rs13137909	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13144225	0.83[ASN][1000 genomes]
rs13144226	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1501373	0.81[ASN][1000 genomes]
rs17002824	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17002828	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1813725	0.85[ASN][1000 genomes]
rs2008222	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2030463	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2102116	0.94[EUR][1000 genomes]
rs2134048	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2173869	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2866688	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2866690	0.87[EUR][1000 genomes]
rs2903291	0.83[ASN][1000 genomes]
rs3205281	0.94[EUR][1000 genomes]
rs4304001	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4388114	0.84[EUR][1000 genomes]
rs4410552	0.85[EUR][1000 genomes]
rs4472161	0.94[EUR][1000 genomes]
rs4541532	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4607246	0.84[EUR][1000 genomes]
rs4859872	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4859878	0.83[ASN][1000 genomes]
rs55673370	0.84[EUR][1000 genomes]
rs57501818	0.84[EUR][1000 genomes]
rs58358199	0.84[EUR][1000 genomes]
rs60135456	0.84[EUR][1000 genomes]
rs6533217	0.94[EUR][1000 genomes]
rs6533226	0.94[EUR][1000 genomes]
rs6533269	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6533270	0.83[ASN][1000 genomes]
rs6533271	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6533272	0.83[ASN][1000 genomes]
rs6533274	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6817305	0.85[EUR][1000 genomes]
rs6817823	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6823465	0.94[EUR][1000 genomes]
rs6827822	0.84[EUR][1000 genomes]
rs6828302	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6833179	0.94[EUR][1000 genomes]
rs6836627	0.83[EUR][1000 genomes]
rs6838630	0.84[EUR][1000 genomes]
rs6839504	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6849922	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6850049	0.83[ASN][1000 genomes]
rs6850111	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6857067	0.83[ASN][1000 genomes]
rs72868269	0.85[EUR][1000 genomes]
rs73827437	0.85[EUR][1000 genomes]
rs73827451	0.84[EUR][1000 genomes]
rs7661064	0.84[EUR][1000 genomes]
rs7674744	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7675586	0.83[EUR][1000 genomes]
rs7687812	0.84[EUR][1000 genomes]
rs7689226	0.84[EUR][1000 genomes]
rs7692075	0.84[EUR][1000 genomes]
rs9996218	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv594700	chr4:78738089-78740601	Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv3451287	chr4:78739278-78741226	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv3340867	chr4:78739453-78742301	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6829203	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs6829203	CNOT6L	cis	Artery Tibial	GTEx
rs6829203	CNOT6L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78737000-78742400	Active TSS	Thymus	Thymus
2	chr4:78738600-78742000	Active TSS	Primary T cells fromperipheralblood	blood
3	chr4:78738600-78742000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:78738600-78742200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:78738600-78742200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:78738600-78742200	Active TSS	Fetal Intestine Small	intestine
7	chr4:78738600-78742200	Active TSS	Psoas Muscle	Psoas
8	chr4:78738600-78742200	Active TSS	NHLF	lung
9	chr4:78738600-78742600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr4:78738600-78742600	Active TSS	Right Atrium	heart
11	chr4:78738800-78742200	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr4:78738800-78742200	Active TSS	Small Intestine	intestine
13	chr4:78738800-78742400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:78738800-78742400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:78738800-78742400	Active TSS	Fetal Intestine Large	intestine
16	chr4:78738800-78742400	Active TSS	Fetal Muscle Trunk	muscle
17	chr4:78738800-78742400	Active TSS	Left Ventricle	heart
18	chr4:78738800-78742400	Active TSS	Pancreas	Pancrea
19	chr4:78738800-78742400	Active TSS	Right Ventricle	heart
20	chr4:78738800-78742800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:78739000-78741800	Active TSS	HMEC	breast
22	chr4:78739000-78742000	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr4:78739000-78742000	Active TSS	Fetal Thymus	thymus
24	chr4:78739000-78742000	Active TSS	Ovary	ovary
25	chr4:78739000-78742000	Active TSS	HSMM	muscle
26	chr4:78739000-78742200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:78739000-78742200	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr4:78739000-78742400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:78739000-78742600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:78739000-78742600	Active TSS	Esophagus	oesophagus
31	chr4:78739000-78742800	Active TSS	Aorta	Aorta
32	chr4:78739200-78740200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr4:78739200-78740400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:78739200-78740600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:78739200-78741600	Active TSS	HSMMtube	muscle
36	chr4:78739200-78741800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:78739200-78741800	Active TSS	Fetal Muscle Leg	muscle
38	chr4:78739200-78741800	Active TSS	Gastric	stomach
39	chr4:78739200-78741800	Active TSS	Lung	lung
40	chr4:78739200-78741800	Active TSS	NHEK	skin
41	chr4:78739200-78742000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:78739200-78742000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:78739200-78742000	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr4:78739200-78742000	Active TSS	Primary T cells from cord blood	blood
45	chr4:78739200-78742000	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr4:78739200-78742000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:78739200-78742000	Active TSS	Brain Anterior Caudate	brain
48	chr4:78739200-78742000	Active TSS	Brain Cingulate Gyrus	brain
49	chr4:78739200-78742000	Active TSS	Brain Hippocampus Middle	brain
50	chr4:78739200-78742000	Active TSS	Duodenum Mucosa	Duodenum

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