Variant report

Variant	rs4850895
Chromosome Location	chr2:99644472-99644473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10496334	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10496335	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11123760	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11123767	0.83[ASN][1000 genomes]
rs12619096	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12620997	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17020569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs17022180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17022249	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2277876	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs28794804	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34751553	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35071324	0.83[ASN][1000 genomes]
rs35458525	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3762472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs3791211	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs56691336	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56926889	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57273701	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57462725	0.91[AFR][1000 genomes]
rs58595226	0.84[ASN][1000 genomes]
rs59243842	0.91[AFR][1000 genomes]
rs59252741	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59506582	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60056452	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60516303	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60653099	0.82[ASN][1000 genomes]
rs6749198	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7568749	0.83[ASN][1000 genomes]
rs7608938	0.94[CHB][hapmap];0.86[JPT][hapmap]

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	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
2	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
3	nsv979072	chr2:99613444-99652736	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4850895	LIPT1	cis	Lymphoblastoid	GTEx
rs4850895	LIPT1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99627600-99658800	Weak transcription	Pancreas	Pancrea
2	chr2:99637800-99649000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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