Variant report

Variant	rs12477978
Chromosome Location	chr2:99646661-99646662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10153745	0.87[AMR][1000 genomes]
rs10165534	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170063	0.90[EUR][1000 genomes]
rs10179043	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10181422	0.88[EUR][1000 genomes]
rs10193019	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10193113	0.84[EUR][1000 genomes]
rs10196680	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10202452	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10865029	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11123761	0.92[ASN][1000 genomes]
rs11123762	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11123763	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11123764	0.82[ASN][1000 genomes]
rs11123765	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11123766	0.82[ASN][1000 genomes]
rs1115756	0.88[EUR][1000 genomes]
rs1115757	0.89[EUR][1000 genomes]
rs11677247	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11678456	0.92[ASN][1000 genomes]
rs11684507	0.84[AFR][1000 genomes]
rs11685759	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11692699	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11693427	0.86[ASN][1000 genomes]
rs11695379	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11695751	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11890338	0.84[AFR][1000 genomes]
rs11900670	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12464710	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12467679	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12470471	0.87[EUR][1000 genomes]
rs12473029	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12477754	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12619780	0.88[AFR][1000 genomes]
rs12992218	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12995473	0.82[ASN][1000 genomes]
rs13004491	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13008496	0.83[AFR][1000 genomes]
rs13018891	0.82[ASN][1000 genomes]
rs13020339	0.86[ASN][1000 genomes]
rs13022329	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13023744	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13035311	0.92[ASN][1000 genomes]
rs13396358	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13407840	0.90[EUR][1000 genomes]
rs13412640	0.84[AMR][1000 genomes]
rs13412764	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13422604	0.83[EUR][1000 genomes]
rs1349778	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1453564	0.90[EUR][1000 genomes]
rs1530996	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1563106	0.81[EUR][1000 genomes]
rs1563107	0.81[EUR][1000 genomes]
rs1563108	0.81[EUR][1000 genomes]
rs1580068	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17708218	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17708262	0.86[EUR][1000 genomes]
rs1993230	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2045057	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2084988	0.90[EUR][1000 genomes]
rs2171362	0.81[AFR][1000 genomes]
rs2309524	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2309581	0.81[ASN][1000 genomes]
rs2516827	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2516828	0.82[ASN][1000 genomes]
rs2516829	0.82[ASN][1000 genomes]
rs2516832	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2516834	0.84[ASN][1000 genomes]
rs2516836	0.81[AFR][1000 genomes]
rs2632260	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2632261	0.82[ASN][1000 genomes]
rs2632277	0.84[ASN][1000 genomes]
rs2632284	0.84[ASN][1000 genomes]
rs28648058	0.86[EUR][1000 genomes]
rs2964969	0.82[ASN][1000 genomes]
rs2969379	0.84[ASN][1000 genomes]
rs34252185	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34766932	0.86[ASN][1000 genomes]
rs35001733	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs36071868	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4340581	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4346438	0.84[EUR][1000 genomes]
rs4402818	0.92[ASN][1000 genomes]
rs4585080	0.87[EUR][1000 genomes]
rs4588238	0.82[ASN][1000 genomes]
rs4622780	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851179	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4851183	0.91[EUR][1000 genomes]
rs4851187	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62154638	0.91[EUR][1000 genomes]
rs6542846	0.90[EUR][1000 genomes]
rs6542852	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542858	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542863	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6542864	0.86[ASN][1000 genomes]
rs6542865	0.82[ASN][1000 genomes]
rs6542869	0.81[ASN][1000 genomes]
rs6704766	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6712704	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6717723	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6717729	0.82[ASN][1000 genomes]
rs6721535	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6722164	0.88[EUR][1000 genomes]
rs6724476	0.91[EUR][1000 genomes]
rs6726618	0.82[AFR][1000 genomes]
rs6732579	0.89[EUR][1000 genomes]
rs6735801	0.90[EUR][1000 genomes]
rs6736064	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6737257	0.87[EUR][1000 genomes]
rs6739579	0.86[ASN][1000 genomes]
rs6740035	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6740054	0.90[EUR][1000 genomes]
rs6740267	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6743355	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6751927	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6753650	0.92[AFR][1000 genomes]
rs6754843	0.87[EUR][1000 genomes]
rs6759354	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs720228	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72957109	0.83[EUR][1000 genomes]
rs7558239	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7570657	0.87[EUR][1000 genomes]
rs7571390	0.91[EUR][1000 genomes]
rs7577477	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7584809	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7586608	0.88[EUR][1000 genomes]
rs7591794	0.90[EUR][1000 genomes]
rs7599427	0.83[EUR][1000 genomes]
rs7604557	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7605734	0.91[EUR][1000 genomes]
rs7606635	0.91[EUR][1000 genomes]
rs896886	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9308816	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs972768	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9808541	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9941561	0.82[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12477978	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs12477978	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs12477978	TSGA10	cis	Thyroid	GTEx
rs12477978	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

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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