Variant report

Variant	rs2008222
Chromosome Location	chr4:78732578-78732579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78730446..78732718-chr4:78782584..78784100,2	K562	blood:
2	chr4:78729932..78733750-chr4:78740001..78742243,3	K562	blood:
3	chr4:78731203..78732890-chr4:78737622..78739382,2	K562	blood:
4	chr4:78727738..78737799-chr4:78737984..78742271,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10005741	0.84[ASN][1000 genomes]
rs10007837	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10222901	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1039403	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10856982	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11097935	0.88[ASN][1000 genomes]
rs1156059	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11727993	0.88[ASN][1000 genomes]
rs11939576	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12643960	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13105201	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13111592	0.84[ASN][1000 genomes]
rs13118459	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13137909	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13144225	0.88[ASN][1000 genomes]
rs13144226	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1501373	0.86[ASN][1000 genomes]
rs17002824	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002828	0.90[AFR][1000 genomes]
rs1813725	0.86[ASN][1000 genomes]
rs2030463	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2102116	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2134048	0.81[EUR][1000 genomes]
rs2173869	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2866688	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2903291	0.88[ASN][1000 genomes]
rs3205281	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4304001	0.89[AFR][1000 genomes]
rs4410552	0.83[AFR][1000 genomes]
rs4472161	0.81[EUR][1000 genomes]
rs4541532	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859872	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4859876	0.84[ASN][1000 genomes]
rs4859878	0.88[ASN][1000 genomes]
rs6533217	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6533226	0.81[EUR][1000 genomes]
rs6533239	0.81[ASN][1000 genomes]
rs6533269	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533270	0.88[ASN][1000 genomes]
rs6533271	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533272	0.88[ASN][1000 genomes]
rs6533274	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6817823	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6823465	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6828302	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6829203	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6833179	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6839504	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6849922	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6850049	0.88[ASN][1000 genomes]
rs6850111	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6855336	0.81[ASN][1000 genomes]
rs6857067	0.88[ASN][1000 genomes]
rs72868269	0.82[AFR][1000 genomes]
rs73827437	0.83[AFR][1000 genomes]
rs7655949	0.84[ASN][1000 genomes]
rs7669988	0.84[ASN][1000 genomes]
rs7674744	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7686883	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9996218	0.84[AMR][1000 genomes];0.83[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2008222	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs2008222	CNOT6L	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78716400-78733400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:78718800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:78720800-78735600	Weak transcription	HepG2	liver
4	chr4:78722200-78738600	Weak transcription	HSMM	muscle
5	chr4:78722400-78734800	Weak transcription	Fetal Intestine Large	intestine
6	chr4:78722600-78735800	Weak transcription	A549	lung
7	chr4:78722600-78737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:78722600-78737800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:78722600-78738600	Weak transcription	NHEK	skin
10	chr4:78722600-78739000	Weak transcription	Ovary	ovary
11	chr4:78722600-78739200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:78722800-78736800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:78722800-78738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:78723000-78732600	Enhancers	Primary T cells from cord blood	blood
15	chr4:78723000-78734800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:78723000-78738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:78723200-78738600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:78724000-78735000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:78724000-78736000	Weak transcription	HUVEC	blood vessel
20	chr4:78724000-78736800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:78724200-78733600	Weak transcription	Primary B cells from cord blood	blood
22	chr4:78724400-78735600	Weak transcription	Liver	Liver
23	chr4:78724400-78738600	Weak transcription	Colonic Mucosa	Colon
24	chr4:78724800-78732800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:78724800-78738600	Weak transcription	Brain Substantia Nigra	brain
26	chr4:78725000-78732800	Weak transcription	Small Intestine	intestine
27	chr4:78725600-78734800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:78725800-78736800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:78725800-78738600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr4:78727200-78737800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:78727400-78732600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:78727400-78733000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:78727400-78735600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:78727400-78735800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:78727400-78735800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:78727800-78732800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr4:78728600-78733800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr4:78728600-78738600	Weak transcription	Psoas Muscle	Psoas
39	chr4:78728800-78736600	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:78728800-78738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:78729000-78736600	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:78730400-78738600	Weak transcription	K562	blood
43	chr4:78731200-78733200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:78731400-78733200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr4:78731800-78733000	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr4:78731800-78733200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr4:78731800-78733200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:78732000-78733200	Genic enhancers	Dnd41	blood
49	chr4:78732000-78734000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:78732200-78732800	Weak transcription	Right Atrium	heart

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