Variant report

Variant	rs12992214
Chromosome Location	chr2:99466337-99466338
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10169003	0.83[ASN][1000 genomes]
rs10181972	0.85[ASN][1000 genomes]
rs10188156	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10202643	0.84[CEU][hapmap]
rs11887536	0.80[ASN][1000 genomes]
rs11900176	0.91[CEU][hapmap]
rs12712033	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12712034	0.83[CEU][hapmap]
rs12712035	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12712037	0.91[CEU][hapmap]
rs12990579	0.92[CEU][hapmap]
rs13004923	0.85[ASN][1000 genomes]
rs1356424	0.80[AMR][1000 genomes]
rs1581250	0.85[ASN][1000 genomes]
rs1878585	0.85[ASN][1000 genomes]
rs1949424	0.88[ASN][1000 genomes]
rs1983352	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2280142	0.83[CEU][hapmap]
rs2280256	0.81[AMR][1000 genomes]
rs4263159	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4850888	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4851162	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4851163	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6542837	0.83[CEU][hapmap]
rs6542838	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6711022	0.81[AMR][1000 genomes]
rs6713991	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6726156	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739097	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752025	0.81[ASN][1000 genomes]
rs7560696	0.84[CEU][hapmap]
rs7579189	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7593332	0.89[ASN][1000 genomes]
rs981601	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs981602	0.81[CEU][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[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	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	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12992214	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:99456200-99473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:99463400-99485400	Weak transcription	Gastric	stomach
5	chr2:99465400-99466400	Enhancers	HepG2	liver
6	chr2:99466000-99468800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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