Variant report

Variant	rs6753650
Chromosome Location	chr2:99706817-99706818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 187 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:184)

rs_ID	r²[population]
rs10164941	0.81[ASN][1000 genomes]
rs10165534	0.84[AFR][1000 genomes]
rs10167390	0.95[ASN][1000 genomes]
rs10170063	0.92[ASN][1000 genomes]
rs10181422	0.83[ASN][1000 genomes]
rs10196680	0.84[AFR][1000 genomes]
rs1044575	0.87[EUR][1000 genomes]
rs10865029	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11123761	0.91[EUR][1000 genomes]
rs11123762	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11123763	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11123764	0.91[EUR][1000 genomes]
rs11123765	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11123766	0.88[EUR][1000 genomes]
rs11123770	0.86[EUR][1000 genomes]
rs1115756	0.95[ASN][1000 genomes]
rs1115757	0.95[ASN][1000 genomes]
rs1133977	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133978	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674894	0.84[EUR][1000 genomes]
rs11677247	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11677321	0.83[EUR][1000 genomes]
rs11678456	0.91[EUR][1000 genomes]
rs11683107	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11683188	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11684507	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11684610	0.81[AFR][1000 genomes]
rs11685759	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11688004	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689265	0.82[EUR][1000 genomes]
rs11692336	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11692669	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11692699	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11693427	0.82[AFR][1000 genomes]
rs11695379	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11695751	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11883676	0.88[EUR][1000 genomes]
rs11890338	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11895749	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11900670	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11903311	0.92[ASN][1000 genomes]
rs12464710	0.92[AFR][1000 genomes]
rs12470471	0.98[ASN][1000 genomes]
rs12473029	0.83[AFR][1000 genomes]
rs12477754	0.84[AFR][1000 genomes]
rs12477978	0.92[AFR][1000 genomes]
rs12613624	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12619780	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621007	0.82[EUR][1000 genomes]
rs12987548	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991189	0.82[EUR][1000 genomes]
rs12992218	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12992930	0.88[EUR][1000 genomes]
rs12995473	0.88[EUR][1000 genomes]
rs13000731	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13004491	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13008171	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13008496	0.82[AFR][1000 genomes]
rs13009147	0.86[EUR][1000 genomes]
rs13018891	0.89[EUR][1000 genomes]
rs13020339	0.87[EUR][1000 genomes]
rs13022329	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13023501	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13023744	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13030961	0.82[EUR][1000 genomes]
rs13031919	0.81[EUR][1000 genomes]
rs13033012	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13035311	0.91[EUR][1000 genomes]
rs13035357	0.83[ASN][1000 genomes]
rs13396358	0.81[AFR][1000 genomes]
rs13407840	0.84[ASN][1000 genomes]
rs13412764	0.81[AFR][1000 genomes]
rs1349779	0.92[AFR][1000 genomes]
rs13798	0.87[EUR][1000 genomes]
rs1453563	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1453564	0.83[ASN][1000 genomes]
rs1530996	0.81[AFR][1000 genomes]
rs1563106	0.98[ASN][1000 genomes]
rs1563107	0.98[ASN][1000 genomes]
rs1563108	0.98[ASN][1000 genomes]
rs1580068	0.92[AFR][1000 genomes]
rs17708218	0.95[AFR][1000 genomes]
rs17708262	0.97[ASN][1000 genomes]
rs17759607	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1993230	0.91[AFR][1000 genomes]
rs2045057	0.91[AFR][1000 genomes]
rs2084988	0.91[ASN][1000 genomes]
rs2171359	0.87[EUR][1000 genomes]
rs2171362	0.83[EUR][1000 genomes]
rs2309524	0.89[AFR][1000 genomes]
rs2309581	0.88[EUR][1000 genomes]
rs2516827	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2516828	0.88[EUR][1000 genomes]
rs2516829	0.88[EUR][1000 genomes]
rs2516830	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516832	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2516833	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516834	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2516835	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2516836	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2632260	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2632261	0.88[EUR][1000 genomes]
rs2632277	0.83[EUR][1000 genomes]
rs2632283	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2632284	0.81[EUR][1000 genomes]
rs28648058	0.98[ASN][1000 genomes]
rs2964969	0.88[EUR][1000 genomes]
rs2969379	0.83[EUR][1000 genomes]
rs34252185	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34272114	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34766932	0.90[EUR][1000 genomes]
rs35461437	0.85[EUR][1000 genomes]
rs36071868	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4340581	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4347885	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4402818	0.91[EUR][1000 genomes]
rs4585080	0.81[ASN][1000 genomes]
rs4588238	0.90[EUR][1000 genomes]
rs4850897	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851179	0.81[AFR][1000 genomes]
rs4851183	0.89[ASN][1000 genomes]
rs4851187	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4851188	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62154638	0.92[ASN][1000 genomes]
rs6542846	0.83[ASN][1000 genomes]
rs6542852	0.81[AFR][1000 genomes]
rs6542858	0.90[AFR][1000 genomes]
rs6542863	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6542864	0.92[EUR][1000 genomes]
rs6542865	0.89[EUR][1000 genomes]
rs6542866	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542868	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542869	0.87[EUR][1000 genomes]
rs6542870	0.88[EUR][1000 genomes]
rs6704766	0.92[AFR][1000 genomes]
rs6707462	0.87[ASN][1000 genomes]
rs6708576	0.87[EUR][1000 genomes]
rs6708878	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6712704	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6717723	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6717729	0.88[EUR][1000 genomes]
rs6722164	0.83[ASN][1000 genomes]
rs6724476	0.89[ASN][1000 genomes]
rs6726618	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6727749	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6735801	0.92[ASN][1000 genomes]
rs6736064	0.92[AFR][1000 genomes]
rs6737257	0.96[ASN][1000 genomes]
rs6739579	0.92[EUR][1000 genomes]
rs6740035	0.81[AFR][1000 genomes]
rs6740054	0.84[ASN][1000 genomes]
rs6740267	0.81[AFR][1000 genomes]
rs6741773	0.85[EUR][1000 genomes]
rs6743355	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6751927	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6753063	0.88[EUR][1000 genomes]
rs6754843	0.97[ASN][1000 genomes]
rs6756650	0.88[EUR][1000 genomes]
rs6757661	0.88[EUR][1000 genomes]
rs6759354	0.84[AFR][1000 genomes]
rs720228	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs720229	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7349217	0.85[EUR][1000 genomes]
rs7558004	0.87[EUR][1000 genomes]
rs7558239	0.91[AFR][1000 genomes]
rs7570657	0.92[ASN][1000 genomes]
rs7571390	0.89[ASN][1000 genomes]
rs7572660	0.88[EUR][1000 genomes]
rs7577477	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7584809	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7586608	0.83[ASN][1000 genomes]
rs7588059	0.84[ASN][1000 genomes]
rs7591794	0.84[ASN][1000 genomes]
rs7604557	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7605734	0.92[ASN][1000 genomes]
rs7605843	0.87[EUR][1000 genomes]
rs7606635	0.92[ASN][1000 genomes]
rs7608938	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8179690	0.87[EUR][1000 genomes]
rs896886	0.92[AFR][1000 genomes]
rs9308816	0.84[AFR][1000 genomes]
rs972768	0.89[AFR][1000 genomes]
rs9808541	0.89[AFR][1000 genomes]
rs9941561	0.88[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	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	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6753650	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs6753650	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6753650	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs6753650	LIPT1	cis	intralobular white matter	BrainEAC
rs6753650	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6753650	LIPT1	cis	occipital cortex	BrainEAC
rs6753650	LIPT1	cis	brain	BrainEAC
rs6753650	TSGA10	cis	Esophagus Mucosa	GTEx
rs6753650	TSGA10	cis	Thyroid	GTEx
rs6753650	LIPT1	cis	thalamus	BrainEAC
rs6753650	LIPT1	cis	hippocampus	BrainEAC
rs6753650	LIPT1	cis	temporal cortex	BrainEAC
rs6753650	LIPT1	cis	cerebellar cortex	BrainEAC
rs6753650	TSGA10	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99700400-99707400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:99703400-99717800	Weak transcription	Brain Cingulate Gyrus	brain

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