Variant report

Variant	rs4549398
Chromosome Location	chr4:147052708-147052709
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10000407	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519776	0.81[EUR][1000 genomes]
rs11100919	0.81[EUR][1000 genomes]
rs11721873	0.81[EUR][1000 genomes]
rs11723069	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11724307	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725678	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11728525	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728609	0.81[EUR][1000 genomes]
rs11729787	0.81[EUR][1000 genomes]
rs11730306	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11733347	0.81[EUR][1000 genomes]
rs11940961	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12152657	0.81[EUR][1000 genomes]
rs12152709	0.81[EUR][1000 genomes]
rs17021106	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17021217	0.81[EUR][1000 genomes]
rs17756056	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756234	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17757522	0.83[EUR][1000 genomes]
rs17757685	0.81[EUR][1000 genomes]
rs17757715	0.81[EUR][1000 genomes]
rs17758092	0.81[EUR][1000 genomes]
rs17758396	0.80[EUR][1000 genomes]
rs17758420	0.81[EUR][1000 genomes]
rs17814023	0.81[EUR][1000 genomes]
rs17814065	0.81[EUR][1000 genomes]
rs17814503	0.81[EUR][1000 genomes]
rs17814598	0.81[EUR][1000 genomes]
rs1812385	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864371	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2007366	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068009	0.81[EUR][1000 genomes]
rs2115796	0.81[EUR][1000 genomes]
rs2115797	0.81[EUR][1000 genomes]
rs2163171	0.81[EUR][1000 genomes]
rs28393640	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756082	0.81[EUR][1000 genomes]
rs3948408	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4835286	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55736910	0.81[EUR][1000 genomes]
rs56174047	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279747	0.81[EUR][1000 genomes]
rs56289966	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56333123	0.81[EUR][1000 genomes]
rs62326764	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326797	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62326804	0.81[EUR][1000 genomes]
rs62326848	0.81[EUR][1000 genomes]
rs6537399	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537400	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	0.81[EUR][1000 genomes]
rs6821066	0.81[EUR][1000 genomes]
rs6821479	0.81[EUR][1000 genomes]
rs6824313	0.81[EUR][1000 genomes]
rs6832576	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838458	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6839123	0.81[EUR][1000 genomes]
rs6839141	0.81[EUR][1000 genomes]
rs6844381	0.81[EUR][1000 genomes]
rs6856647	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72727922	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7657269	0.83[EUR][1000 genomes]
rs7695415	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745	0.81[EUR][1000 genomes]
rs919483	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4549398	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs4549398	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs4549398	RP11-6L6.2	cis	Muscle Skeletal	GTEx
rs4549398	RP11-6L6.2	cis	lung	GTEx
rs4549398	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4549398	RP11-6L6.2	cis	Esophagus Muscularis	GTEx
rs4549398	RP11-6L6.2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147045800-147055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:147052400-147053200	Enhancers	GM12878-XiMat	blood
3	chr4:147052600-147056000	Weak transcription	Right Atrium	heart

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