Variant report

Variant	rs12643960
Chromosome Location	chr4:78655671-78655672
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	chr4:78649825..78652816-chr4:78654825..78657424,2	K562	blood:
2	chr4:78655466..78657702-chr4:78779436..78782397,2	K562	blood:

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10005741	0.93[ASN][1000 genomes]
rs10007837	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1010728	0.86[AMR][1000 genomes]
rs10222901	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1039403	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10428319	0.82[AMR][1000 genomes]
rs10856982	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10856991	0.82[AMR][1000 genomes]
rs11097900	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11097935	0.88[ASN][1000 genomes]
rs11097965	0.88[AMR][1000 genomes]
rs1156059	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11727993	0.88[ASN][1000 genomes]
rs11731374	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11737353	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11939576	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12108312	0.86[AMR][1000 genomes]
rs12510593	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13105201	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13111592	0.93[ASN][1000 genomes]
rs13118459	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13128914	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13137909	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138341	0.95[ASN][1000 genomes]
rs13144225	0.88[ASN][1000 genomes]
rs13144226	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1501373	0.90[ASN][1000 genomes]
rs17002824	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17002828	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1813725	0.86[ASN][1000 genomes]
rs2008222	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2030463	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2102116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2134048	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173869	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2174078	0.86[AMR][1000 genomes]
rs2174080	0.86[AMR][1000 genomes]
rs2866444	0.84[ASN][1000 genomes]
rs2866688	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2866689	0.96[ASN][1000 genomes]
rs2866690	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2903291	0.88[ASN][1000 genomes]
rs3205281	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4304001	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4388114	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4410552	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4472161	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4541532	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4546268	0.82[AMR][1000 genomes]
rs4561950	0.82[AMR][1000 genomes]
rs4607246	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859506	1.00[ASN][1000 genomes]
rs4859871	0.95[ASN][1000 genomes]
rs4859872	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859876	0.93[ASN][1000 genomes]
rs4859878	0.88[ASN][1000 genomes]
rs55673370	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56138517	0.82[AMR][1000 genomes]
rs57501818	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57896992	0.86[AMR][1000 genomes]
rs58358199	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60135456	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6533217	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533226	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533239	0.95[ASN][1000 genomes]
rs6533269	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533270	0.88[ASN][1000 genomes]
rs6533271	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533272	0.88[ASN][1000 genomes]
rs6533274	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6814830	0.80[ASN][1000 genomes]
rs6817305	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6817823	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6821826	0.86[AMR][1000 genomes]
rs6823465	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6827822	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6828302	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6829203	0.94[EUR][1000 genomes]
rs6832015	0.82[AMR][1000 genomes]
rs6833179	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836627	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6838630	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6839504	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6849922	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6850049	0.88[ASN][1000 genomes]
rs6850111	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6854989	0.82[AMR][1000 genomes]
rs6855336	0.95[ASN][1000 genomes]
rs6857067	0.88[ASN][1000 genomes]
rs72868269	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72869573	0.84[AMR][1000 genomes]
rs73827437	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73827451	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7439347	0.82[AMR][1000 genomes]
rs7655949	0.93[ASN][1000 genomes]
rs7656319	0.86[AMR][1000 genomes]
rs7659122	0.82[AMR][1000 genomes]
rs7661064	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7663359	0.82[AMR][1000 genomes]
rs7669988	0.93[ASN][1000 genomes]
rs7671941	0.82[AMR][1000 genomes]
rs7673642	0.86[AMR][1000 genomes]
rs7674744	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675586	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7687170	0.82[AMR][1000 genomes]
rs7687812	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7689226	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7692075	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7693256	0.84[ASN][1000 genomes]
rs885376	0.94[ASN][1000 genomes]
rs9993942	1.00[ASN][1000 genomes]
rs9996218	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv518757	chr4:78637265-78695138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12643960	CNOT6L	cis	Artery Tibial	GTEx
rs12643960	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:78629400-78656200	Weak transcription	Small Intestine	intestine
3	chr4:78630200-78660000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:78631200-78656000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
6	chr4:78636400-78659000	Weak transcription	Psoas Muscle	Psoas
7	chr4:78637400-78661200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:78637400-78673200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:78639200-78661200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:78639400-78671200	Weak transcription	Brain Germinal Matrix	brain
11	chr4:78640200-78656200	Strong transcription	Fetal Thymus	thymus
12	chr4:78640400-78655800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:78640800-78697800	Weak transcription	Stomach Mucosa	stomach
14	chr4:78641000-78665000	Weak transcription	Fetal Brain Male	brain
15	chr4:78643800-78714000	Weak transcription	Lung	lung
16	chr4:78644800-78666600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:78645000-78664000	Weak transcription	A549	lung
18	chr4:78645000-78676600	Weak transcription	Hela-S3	cervix
19	chr4:78645400-78696200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:78645600-78663200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:78645800-78656400	Weak transcription	Fetal Intestine Small	intestine
22	chr4:78645800-78658800	Weak transcription	Fetal Stomach	stomach
23	chr4:78646000-78664000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:78646200-78663800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:78646800-78677200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:78649800-78660800	Weak transcription	HSMM	muscle
27	chr4:78650000-78659200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:78650000-78660200	Weak transcription	Brain Anterior Caudate	brain
29	chr4:78650000-78663200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:78650000-78682400	Weak transcription	Brain Substantia Nigra	brain
31	chr4:78650000-78683800	Weak transcription	NHDF-Ad	bronchial
32	chr4:78650200-78656000	Weak transcription	K562	blood
33	chr4:78650200-78656200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:78650200-78659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:78650200-78659000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:78650200-78659200	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:78650200-78660400	Weak transcription	HMEC	breast
38	chr4:78650200-78661200	Weak transcription	Aorta	Aorta
39	chr4:78650200-78661200	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:78650200-78661200	Weak transcription	Left Ventricle	heart
41	chr4:78650200-78661200	Weak transcription	Ovary	ovary
42	chr4:78650200-78661200	Weak transcription	Pancreas	Pancrea
43	chr4:78650200-78661800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:78650200-78662600	Weak transcription	Right Ventricle	heart
45	chr4:78650200-78663800	Weak transcription	Fetal Brain Female	brain
46	chr4:78650200-78673000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:78650200-78673000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr4:78650200-78697800	Weak transcription	Gastric	stomach
49	chr4:78650200-78697800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:78650200-78702800	Weak transcription	Stomach Smooth Muscle	stomach

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