Variant report

Variant	rs4402818
Chromosome Location	chr2:99717608-99717609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:99717557-99717707	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:99717563-99717707	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB33	chr2:99717493-99717707	HepG2	liver:	n/a	n/a
4	RXRA	chr2:99717548-99717723	HepG2	liver:	n/a	n/a
5	YY1	chr2:99717539-99717775	ECC-1	luminal epithelium:	n/a	n/a
6	REST	chr2:99717552-99717721	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP1	chr2:99717522-99717738	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000231822	TF binding region

Extended variants
information (count: 150 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10165534	0.97[ASN][1000 genomes]
rs10179043	0.98[ASN][1000 genomes]
rs10193019	0.85[ASN][1000 genomes]
rs10196680	0.97[ASN][1000 genomes]
rs1044575	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865029	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123761	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123762	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123763	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123764	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123765	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123766	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123770	0.80[EUR][1000 genomes]
rs1133977	0.86[EUR][1000 genomes]
rs1133978	0.86[EUR][1000 genomes]
rs11677247	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11677321	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11678456	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683107	0.83[EUR][1000 genomes]
rs11683188	0.87[EUR][1000 genomes]
rs11684507	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11684610	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11685759	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688004	0.87[EUR][1000 genomes]
rs11689265	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11692336	0.86[EUR][1000 genomes]
rs11692699	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11693427	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11695379	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11695751	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883676	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11890338	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11895749	0.86[EUR][1000 genomes]
rs11900670	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464710	0.93[ASN][1000 genomes]
rs12467679	0.97[ASN][1000 genomes]
rs12473029	0.95[ASN][1000 genomes]
rs12477754	0.97[ASN][1000 genomes]
rs12477978	0.92[ASN][1000 genomes]
rs12613624	0.87[EUR][1000 genomes]
rs12619780	0.86[EUR][1000 genomes]
rs12621007	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12987548	0.85[EUR][1000 genomes]
rs12992218	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12992930	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12995473	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12999417	0.81[EUR][1000 genomes]
rs13000731	0.83[EUR][1000 genomes]
rs13004491	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13008171	0.86[EUR][1000 genomes]
rs13008496	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13009147	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13012481	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13018891	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13020339	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13022329	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13023479	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13023744	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13025880	0.83[AFR][1000 genomes]
rs13026928	0.85[EUR][1000 genomes]
rs13030961	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13033012	0.83[EUR][1000 genomes]
rs13035311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349778	0.97[ASN][1000 genomes]
rs1349779	0.95[ASN][1000 genomes]
rs13798	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1453563	0.87[EUR][1000 genomes]
rs1580068	0.97[ASN][1000 genomes]
rs17708218	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17759607	0.87[EUR][1000 genomes]
rs1993230	1.00[ASN][1000 genomes]
rs2045057	1.00[ASN][1000 genomes]
rs2171359	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2171362	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2309524	1.00[ASN][1000 genomes]
rs2309581	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2516827	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516828	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516829	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516830	0.83[EUR][1000 genomes]
rs2516832	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516833	0.83[EUR][1000 genomes]
rs2516834	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2516835	0.84[EUR][1000 genomes]
rs2516836	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2632260	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2632261	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2632277	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2632283	0.84[EUR][1000 genomes]
rs2632284	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2964969	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2969379	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34252185	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34272114	0.87[EUR][1000 genomes]
rs34766932	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35461437	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36071868	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4340581	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4347885	0.82[EUR][1000 genomes]
rs4588238	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4622780	0.97[ASN][1000 genomes]
rs4850897	0.83[EUR][1000 genomes]
rs4851187	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851188	0.84[EUR][1000 genomes]
rs6542852	0.93[ASN][1000 genomes]
rs6542858	0.97[ASN][1000 genomes]
rs6542863	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542864	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542865	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542866	0.84[EUR][1000 genomes]
rs6542868	0.83[EUR][1000 genomes]
rs6542869	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542870	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6704766	0.97[ASN][1000 genomes]
rs6708576	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6708878	0.83[EUR][1000 genomes]
rs6712704	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717723	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717729	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6726618	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6727749	0.83[EUR][1000 genomes]
rs6736064	0.97[ASN][1000 genomes]
rs6739579	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6741773	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6743355	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6751927	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6753063	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6753650	0.91[EUR][1000 genomes]
rs6756650	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6757661	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6759354	0.97[ASN][1000 genomes]
rs720228	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs720229	0.86[EUR][1000 genomes]
rs7349217	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558004	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558239	0.93[ASN][1000 genomes]
rs7572660	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7577477	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584809	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7604557	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605843	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7608938	0.83[EUR][1000 genomes]
rs8179690	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs896886	0.97[ASN][1000 genomes]
rs9308816	0.97[ASN][1000 genomes]
rs972768	1.00[ASN][1000 genomes]
rs9808541	0.92[ASN][1000 genomes]
rs9941561	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4402818	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs4402818	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs4402818	TSGA10	cis	Esophagus Mucosa	GTEx
rs4402818	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs4402818	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs4402818	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs4402818	TSGA10	cis	Thyroid	GTEx
rs4402818	TSGA10	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99703400-99717800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99712600-99718000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:99717600-99717800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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