Variant report

Variant	rs4346438
Chromosome Location	chr2:99606346-99606347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10170063	0.92[EUR][1000 genomes]
rs10181422	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1115756	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1115757	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11903311	0.82[EUR][1000 genomes]
rs12470471	0.89[EUR][1000 genomes]
rs12473029	0.84[EUR][1000 genomes]
rs12477978	0.84[EUR][1000 genomes]
rs13407840	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1349779	0.84[EUR][1000 genomes]
rs1453564	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1530996	0.83[EUR][1000 genomes]
rs1563106	0.83[EUR][1000 genomes]
rs1563107	0.83[EUR][1000 genomes]
rs1563108	0.83[EUR][1000 genomes]
rs17708262	0.90[EUR][1000 genomes]
rs2084988	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28648058	0.90[EUR][1000 genomes]
rs4585080	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4851179	0.85[EUR][1000 genomes]
rs4851183	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62154638	0.93[EUR][1000 genomes]
rs6542846	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6722164	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6724476	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6735801	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6737257	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6740054	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6754843	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72957109	0.81[EUR][1000 genomes]
rs7570657	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7571390	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7586608	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7591794	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7599427	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7605734	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7606635	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv978937	chr2:99590098-99612582	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
6	nsv2844	chr2:99594062-99638761	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4346438	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs4346438	TSGA10	cis	Thyroid	GTEx
rs4346438	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs4346438	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99604800-99607000	Weak transcription	Right Atrium	heart

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