Variant report

Variant	rs13138341
Chromosome Location	chr4:78629109-78629110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10005741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10007837	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs10222901	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1039403	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs1039467	0.84[AMR][1000 genomes]
rs10856982	0.84[ASN][1000 genomes]
rs11097900	0.81[ASN][1000 genomes]
rs11097935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11097965	0.85[CHB][hapmap]
rs11721383	0.89[CEU][hapmap];0.92[CHB][hapmap];0.81[AMR][1000 genomes]
rs11723029	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11723221	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs11727993	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11729703	0.81[AMR][1000 genomes]
rs11730329	0.87[AMR][1000 genomes]
rs11730403	0.87[AMR][1000 genomes]
rs11731374	1.00[CHB][hapmap]
rs11732039	0.84[AMR][1000 genomes]
rs11733759	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs11734428	0.84[AMR][1000 genomes]
rs11737353	1.00[CHB][hapmap]
rs11737861	1.00[CHB][hapmap]
rs12510593	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12643960	0.95[ASN][1000 genomes]
rs13105201	0.96[ASN][1000 genomes]
rs13111592	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13118459	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs13128914	0.96[ASN][1000 genomes]
rs13131896	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13137909	0.84[ASN][1000 genomes]
rs13144225	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13144226	0.84[ASN][1000 genomes]
rs1402626	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1501373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1521419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1554457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17002823	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17002825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17002831	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1813725	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1814033	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1847216	0.84[AMR][1000 genomes]
rs1980266	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2030463	0.86[ASN][1000 genomes]
rs2062637	0.84[JPT][hapmap]
rs2102116	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2134048	0.92[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs2134459	0.84[AMR][1000 genomes]
rs2173869	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2866444	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2866688	1.00[CHB][hapmap]
rs2866689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2866690	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs28796999	0.84[AMR][1000 genomes]
rs28891692	0.84[AMR][1000 genomes]
rs2903291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3205281	0.92[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs4078523	0.87[AMR][1000 genomes]
rs4304001	1.00[CHB][hapmap]
rs4365752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4388114	1.00[CHB][hapmap]
rs4410552	1.00[CHB][hapmap]
rs4417999	0.81[AMR][1000 genomes]
rs4472161	0.99[ASN][1000 genomes]
rs4541532	0.84[ASN][1000 genomes]
rs4859506	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859872	0.90[ASN][1000 genomes]
rs4859876	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55694923	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55886549	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57221952	0.84[AMR][1000 genomes]
rs57246363	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57868780	0.81[AMR][1000 genomes]
rs58054752	0.84[AMR][1000 genomes]
rs58218398	0.84[AMR][1000 genomes]
rs6533217	1.00[ASN][1000 genomes]
rs6533226	0.95[ASN][1000 genomes]
rs6533239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533269	0.84[ASN][1000 genomes]
rs6533270	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6533271	0.84[ASN][1000 genomes]
rs6533272	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6533274	0.80[ASN][1000 genomes]
rs6533290	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6533358	0.80[AMR][1000 genomes]
rs6533359	0.84[AMR][1000 genomes]
rs6817305	1.00[CHB][hapmap]
rs6817823	0.84[ASN][1000 genomes]
rs6822317	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6823465	0.88[ASN][1000 genomes]
rs6827822	1.00[CHB][hapmap]
rs6833179	0.90[ASN][1000 genomes]
rs6839504	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs6849922	0.80[ASN][1000 genomes]
rs6850049	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6850111	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs6850590	0.84[AMR][1000 genomes]
rs6855336	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6857067	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73827459	0.84[AMR][1000 genomes]
rs73827460	0.84[AMR][1000 genomes]
rs7655949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7657658	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7661064	1.00[CHB][hapmap]
rs7669988	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7674744	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs7687812	1.00[CHB][hapmap]
rs7693256	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs885376	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9993942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13138341	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78617400-78634400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:78621000-78631200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:78621200-78633200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:78621200-78635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:78621400-78645800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:78621600-78643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:78622000-78638800	Weak transcription	NHEK	skin
8	chr4:78622400-78630800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:78622800-78629800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:78623400-78633000	Weak transcription	HSMM	muscle
11	chr4:78623800-78633000	Weak transcription	HSMMtube	muscle
12	chr4:78625000-78631200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:78625000-78638800	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:78625200-78631400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:78626400-78644400	Weak transcription	Placenta	Placenta
16	chr4:78626400-78645200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:78626800-78631200	Weak transcription	Primary T cells from cord blood	blood
18	chr4:78628200-78631400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:78628400-78631800	Weak transcription	Thymus	Thymus
20	chr4:78628400-78632800	Weak transcription	Fetal Lung	lung
21	chr4:78628400-78636800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:78628400-78638200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:78628400-78638800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:78628400-78648400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:78628600-78636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:78628600-78641400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:78629000-78629200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:78629000-78649400	Weak transcription	HMEC	breast

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