Variant report

Variant	rs1039403
Chromosome Location	chr4:78634131-78634132
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78623199..78625364-chr4:78633435..78635533,2	K562	blood:

Variant related genes	Relation type
ENSG00000221711	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10005741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10007837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1010728	0.86[AMR][1000 genomes]
rs10222901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10428319	0.82[AMR][1000 genomes]
rs10856982	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11097900	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11097935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11097965	0.90[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes]
rs1156059	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11721383	0.92[CHB][hapmap]
rs11723221	1.00[CHB][hapmap]
rs11727993	0.85[ASN][1000 genomes]
rs11731374	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11733759	1.00[CHB][hapmap]
rs11737353	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11737861	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs11939576	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12108312	0.86[AMR][1000 genomes]
rs12510593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12643960	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13105201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111592	0.89[ASN][1000 genomes]
rs13118459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13128914	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137909	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13138341	0.96[ASN][1000 genomes]
rs13144225	0.85[ASN][1000 genomes]
rs13144226	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1501373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1521419	1.00[CHB][hapmap]
rs1554457	1.00[CHB][hapmap]
rs17002824	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17002825	1.00[CHB][hapmap]
rs17002828	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17002829	1.00[CHB][hapmap]
rs1813725	0.83[ASN][1000 genomes]
rs1814033	0.85[CHB][hapmap]
rs2008222	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2030463	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2062637	0.93[JPT][hapmap]
rs2102116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2134048	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2173869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2174078	0.86[AMR][1000 genomes]
rs2174080	0.86[AMR][1000 genomes]
rs2866444	0.81[ASN][1000 genomes]
rs2866688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2866689	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs2866690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3205281	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4304001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4365752	1.00[CHB][hapmap]
rs4388114	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4410552	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4472161	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4541532	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4546268	0.82[AMR][1000 genomes]
rs4561950	0.82[AMR][1000 genomes]
rs4607246	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859506	0.96[ASN][1000 genomes]
rs4859871	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs4859872	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859876	0.89[ASN][1000 genomes]
rs4859878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs55673370	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56138517	0.82[AMR][1000 genomes]
rs57501818	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57896992	0.86[AMR][1000 genomes]
rs58358199	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60135456	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6533217	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533226	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6533269	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533270	0.85[ASN][1000 genomes]
rs6533271	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533272	0.85[ASN][1000 genomes]
rs6533274	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6817305	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6817823	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6821826	0.86[AMR][1000 genomes]
rs6822317	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs6823465	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6827822	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6828302	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6829203	0.94[EUR][1000 genomes]
rs6832015	0.82[AMR][1000 genomes]
rs6833179	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6836627	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6838630	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6839504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6849922	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6850049	0.85[ASN][1000 genomes]
rs6850111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6854989	0.82[AMR][1000 genomes]
rs6855336	0.92[ASN][1000 genomes]
rs6857067	0.85[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	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7439347	0.82[AMR][1000 genomes]
rs7655949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7656319	0.86[AMR][1000 genomes]
rs7657658	1.00[CHB][hapmap]
rs7659122	0.81[AMR][1000 genomes]
rs7661064	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7663359	0.82[AMR][1000 genomes]
rs7669988	0.89[ASN][1000 genomes]
rs7671941	0.82[AMR][1000 genomes]
rs7673642	0.86[AMR][1000 genomes]
rs7674744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7675586	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7687170	0.82[AMR][1000 genomes]
rs7687812	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7689226	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7692075	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7693256	0.81[ASN][1000 genomes]
rs885376	0.98[ASN][1000 genomes]
rs9993942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9996218	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1039403	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs1039403	CNOT6L	cis	Artery Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78617400-78634400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:78621200-78635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:78621400-78645800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:78621600-78643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:78622000-78638800	Weak transcription	NHEK	skin
6	chr4:78625000-78638800	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:78626400-78644400	Weak transcription	Placenta	Placenta
8	chr4:78626400-78645200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:78628400-78636800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:78628400-78638200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:78628400-78638800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:78628400-78648400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:78628600-78636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:78628600-78641400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:78629000-78649400	Weak transcription	HMEC	breast
16	chr4:78629200-78676600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:78629400-78638200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:78629400-78649400	Weak transcription	Spleen	Spleen
19	chr4:78629400-78656200	Weak transcription	Small Intestine	intestine
20	chr4:78629800-78635600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:78630000-78643600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:78630200-78636000	Weak transcription	Primary B cells from cord blood	blood
23	chr4:78630200-78660000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:78630600-78637200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:78631200-78634600	Strong transcription	Primary T cells from cord blood	blood
26	chr4:78631200-78635800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:78631200-78656000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:78631400-78639000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:78631400-78643400	Weak transcription	Gastric	stomach
30	chr4:78631600-78636600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:78631600-78638400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:78631600-78649400	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:78631600-78652600	Weak transcription	Esophagus	oesophagus
34	chr4:78631800-78634800	Strong transcription	Thymus	Thymus
35	chr4:78631800-78635800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:78631800-78638000	Weak transcription	Fetal Intestine Large	intestine
37	chr4:78631800-78638800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr4:78631800-78640800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:78631800-78649400	Weak transcription	Aorta	Aorta
40	chr4:78632000-78637200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:78632000-78651800	Weak transcription	HepG2	liver
42	chr4:78632200-78636600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:78632400-78640600	Weak transcription	Adipose Nuclei	Adipose
44	chr4:78632400-78642800	Weak transcription	Fetal Intestine Small	intestine
45	chr4:78632600-78697800	Weak transcription	Colonic Mucosa	Colon
46	chr4:78632800-78635000	Enhancers	Fetal Lung	lung
47	chr4:78633000-78634200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr4:78633000-78634600	Strong transcription	HSMMtube	muscle
49	chr4:78633000-78637400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:78633200-78634800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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