Variant report

Variant	rs12712033
Chromosome Location	chr2:99457973-99457974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10175560	0.89[EUR][1000 genomes]
rs10188156	0.93[ASN][1000 genomes]
rs11123756	0.85[EUR][1000 genomes]
rs11900176	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11900524	0.89[EUR][1000 genomes]
rs12478574	0.85[EUR][1000 genomes]
rs12712034	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[EUR][1000 genomes]
rs12712035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12712036	0.86[CHB][hapmap]
rs12712037	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs12712040	0.82[EUR][1000 genomes]
rs12990579	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs12992214	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13005148	0.88[EUR][1000 genomes]
rs13389386	0.90[JPT][hapmap]
rs1356424	0.85[JPT][hapmap]
rs1581249	0.82[EUR][1000 genomes]
rs1949424	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1962029	0.85[EUR][1000 genomes]
rs1983352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2276604	0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs2280256	0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4263159	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4499468	0.85[EUR][1000 genomes]
rs4553869	0.85[EUR][1000 genomes]
rs4850888	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4851162	0.95[ASN][1000 genomes]
rs4851163	0.94[ASN][1000 genomes]
rs6542838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6542839	0.86[CHB][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes]
rs6542841	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6704682	0.85[EUR][1000 genomes]
rs6713991	0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6719634	0.86[CHB][hapmap]
rs6733011	0.93[ASN][1000 genomes]
rs6739097	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6752025	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6755640	0.80[EUR][1000 genomes]
rs6757098	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs6760065	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs7565510	0.85[EUR][1000 genomes]
rs7565614	0.89[EUR][1000 genomes]
rs7565736	0.88[EUR][1000 genomes]
rs7579189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7581128	0.81[JPT][hapmap]
rs7590596	0.88[EUR][1000 genomes]
rs7593332	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7608889	0.85[JPT][hapmap]
rs883773	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs885115	0.80[EUR][1000 genomes]
rs981601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs981602	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12712033	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs12712033	TSGA10	cis	Lymphoblastoid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:99450800-99462800	Weak transcription	Gastric	stomach
5	chr2:99453200-99460600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:99454200-99459000	Weak transcription	A549	lung
8	chr2:99456200-99473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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