Variant report

Variant	rs1488425
Chromosome Location	chr3:155838900-155838901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10936024	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11709514	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11716256	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13073556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13078555	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13093154	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs1488426	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1488427	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1906543	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1984473	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3936002	0.81[MEX][hapmap]
rs4234308	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4261831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4359773	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4359774	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4605502	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679760	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679761	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680233	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680234	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680235	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680237	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56231269	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62284939	0.89[ASN][1000 genomes]
rs6441034	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs6441035	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441036	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6441042	0.90[MEX][hapmap]
rs6761966	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6778035	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs6780500	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788449	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793964	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613000	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7617796	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7618820	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629439	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7633081	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645641	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7652981	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9289961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9789968	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9814661	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9816126	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs9838322	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9842620	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9856468	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9861320	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs9862153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9869649	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs9870793	0.88[ASN][1000 genomes]
rs9882088	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[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	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1488425	MLF1	cis	parietal	SCAN
rs1488425	SCARNA7	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155838200-155839000	Enhancers	H9 Cell Line	embryonic stem cell
2	chr3:155838400-155839000	Active TSS	Fetal Muscle Leg	muscle
3	chr3:155838400-155839200	Active TSS	Adipose Nuclei	Adipose
4	chr3:155838600-155839000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
5	chr3:155838600-155839000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:155838800-155850200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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