Variant report

Variant	rs2079108
Chromosome Location	chr4:110236107-110236108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEC24B-1	chr4:110235733-110237291	ENSG00000246774

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10005198	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10007410	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10155246	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11098033	0.81[CHD][hapmap]
rs11933172	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939924	0.91[EUR][1000 genomes]
rs12641197	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12641272	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12650654	0.81[CHD][hapmap]
rs13104799	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13113384	0.94[EUR][1000 genomes]
rs13119700	0.94[EUR][1000 genomes]
rs13126829	0.90[EUR][1000 genomes]
rs13128445	1.00[MEX][hapmap]
rs13138833	0.94[EUR][1000 genomes]
rs1557804	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17842269	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1859144	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1859146	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1859147	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1981540	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1981541	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2079107	1.00[ASN][1000 genomes]
rs2214377	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2346014	0.94[EUR][1000 genomes]
rs28374470	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28463999	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28542804	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28585579	0.94[EUR][1000 genomes]
rs28628718	0.94[EUR][1000 genomes]
rs28749845	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4524460	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60369504	1.00[ASN][1000 genomes]
rs6533426	0.94[EUR][1000 genomes]
rs6825928	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs6827985	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841133	0.94[EUR][1000 genomes]
rs6841222	0.94[EUR][1000 genomes]
rs714586	1.00[MEX][hapmap]
rs7436583	0.81[CHD][hapmap]
rs7436745	0.81[CHD][hapmap]
rs7665024	0.90[EUR][1000 genomes]
rs7673595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7673867	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7675344	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7680752	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7680920	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7684744	0.94[EUR][1000 genomes]
rs7685787	0.94[EUR][1000 genomes]
rs7694523	0.90[EUR][1000 genomes]
rs7695754	1.00[CEU][hapmap]
rs7699247	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs876464	0.94[EUR][1000 genomes]
rs9307329	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9993228	0.94[EUR][1000 genomes]
rs9996165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9996432	0.94[EUR][1000 genomes]
rs9996537	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9996920	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999270	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999278	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999751	0.87[AMR][1000 genomes];0.95[EUR][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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv515893	chr4:110222845-110254841	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110234800-110236200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr4:110235800-110236800	Weak transcription	Psoas Muscle	Psoas

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