Variant report

Variant	rs1976766
Chromosome Location	chr2:99522754-99522755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10172158	0.91[AMR][1000 genomes]
rs10192266	0.82[AMR][1000 genomes]
rs11123755	0.91[AMR][1000 genomes]
rs12468024	0.89[AMR][1000 genomes]
rs12474283	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712038	0.91[AMR][1000 genomes]
rs12712041	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712042	0.81[AMR][1000 genomes]
rs12712043	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13004700	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13005124	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13011428	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13025076	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13025913	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13028500	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1581251	0.91[AMR][1000 genomes]
rs1607256	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4311103	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4850889	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4850890	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4851167	0.91[AMR][1000 genomes]
rs4851170	0.91[AMR][1000 genomes]
rs4851171	0.90[AMR][1000 genomes]
rs4851173	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851174	0.83[AMR][1000 genomes]
rs4851175	0.83[AMR][1000 genomes]
rs4851177	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56125264	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6419564	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542843	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542845	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6714243	0.91[AMR][1000 genomes]
rs6717372	0.90[AMR][1000 genomes]
rs6724477	0.81[AMR][1000 genomes]
rs6739176	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739503	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6742047	0.83[AMR][1000 genomes]
rs7608889	0.90[AMR][1000 genomes]
rs925887	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1976766	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99512000-99526000	Weak transcription	Right Atrium	heart
2	chr2:99513200-99525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:99515200-99524600	Weak transcription	Pancreas	Pancrea
4	chr2:99517600-99526000	Weak transcription	Gastric	stomach
5	chr2:99518800-99525000	Weak transcription	Spleen	Spleen
6	chr2:99519600-99524800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:99520800-99528600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:99521000-99525000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:99521000-99525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:99521000-99525000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:99521000-99525200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:99521000-99526000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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