Variant report

Variant	rs28542730
Chromosome Location	chr4:84489122-84489123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10002139	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10009351	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10012782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721920	0.95[ASN][1000 genomes]
rs11722160	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11723311	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11730975	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11731267	0.93[ASN][1000 genomes]
rs11731336	0.93[ASN][1000 genomes]
rs11733281	0.95[ASN][1000 genomes]
rs11734158	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736724	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737424	0.95[ASN][1000 genomes]
rs12331130	0.95[ASN][1000 genomes]
rs12331142	0.95[ASN][1000 genomes]
rs12331198	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12331205	0.95[ASN][1000 genomes]
rs12331922	0.95[ASN][1000 genomes]
rs17006888	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17353060	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17355300	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17355321	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1965464	0.93[ASN][1000 genomes]
rs28463240	0.95[ASN][1000 genomes]
rs28482178	0.95[ASN][1000 genomes]
rs28504032	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28587748	0.95[ASN][1000 genomes]
rs28615868	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28710332	0.95[ASN][1000 genomes]
rs35434386	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693092	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693093	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55724846	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55839835	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55851819	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56003368	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56191639	0.82[EUR][1000 genomes]
rs56208893	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56394927	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62303966	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62303968	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305330	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305331	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305332	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305333	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305334	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305335	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305336	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62305339	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62305340	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305342	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305343	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6812240	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812267	0.95[ASN][1000 genomes]
rs6835060	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835481	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72654969	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72654977	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72654978	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9307826	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307827	0.96[AFR][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	nsv829994	chr4:84366299-84558316	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv879512	chr4:84374692-85090749	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1010009	chr4:84469896-84882528	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28542730	MAG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:84480200-84489400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr4:84481200-84503200	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:84482800-84490400	Weak transcription	Psoas Muscle	Psoas
4	chr4:84482800-84503400	Weak transcription	Ovary	ovary
5	chr4:84483000-84490600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:84483200-84490600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:84485800-84491000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:84486000-84513000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:84488200-84489600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr4:84488200-84491400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:84488200-84491600	Enhancers	A549	lung
12	chr4:84488600-84516800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:84489000-84489400	Weak transcription	Left Ventricle	heart

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