Variant report

Variant	rs6542863
Chromosome Location	chr2:99725138-99725139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99720605..99722311-chr2:99723972..99725744,2	K562	blood:
2	chr2:99721431..99723129-chr2:99723599..99725832,2	MCF-7	breast:
3	chr2:99724735..99727280-chr2:99755994..99759484,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135951	Chromatin interaction
ENSG00000273045	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10165534	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10179043	0.92[ASN][1000 genomes]
rs10196680	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1044575	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123761	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123763	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123764	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123765	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123766	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123770	0.81[EUR][1000 genomes]
rs1133977	0.87[EUR][1000 genomes]
rs1133978	0.87[EUR][1000 genomes]
rs11677247	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11677321	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11678456	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11683107	0.84[EUR][1000 genomes]
rs11683188	0.87[EUR][1000 genomes]
rs11684507	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11684610	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11685759	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688004	0.87[EUR][1000 genomes]
rs11689265	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11692336	0.87[EUR][1000 genomes]
rs11692669	0.80[EUR][1000 genomes]
rs11692699	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693427	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11695379	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11695751	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11883676	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11890338	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11895749	0.87[EUR][1000 genomes]
rs11900670	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12464710	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12467679	0.90[ASN][1000 genomes]
rs12473029	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12477754	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12477978	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12613624	0.87[EUR][1000 genomes]
rs12619780	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12621007	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12987548	0.86[EUR][1000 genomes]
rs12992218	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12992930	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12995473	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12999417	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13000731	0.83[EUR][1000 genomes]
rs13004491	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13008171	0.87[EUR][1000 genomes]
rs13008496	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13009147	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13012481	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13018891	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13020339	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13022329	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13023479	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13023744	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13026928	0.86[EUR][1000 genomes]
rs13030961	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13033012	0.83[EUR][1000 genomes]
rs13035311	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1349778	0.90[ASN][1000 genomes]
rs1349779	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13798	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1453563	0.87[EUR][1000 genomes]
rs1580068	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17708218	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17759607	0.87[EUR][1000 genomes]
rs1993230	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2045057	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2171359	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2171362	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2309524	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2309581	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516827	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516828	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516829	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516830	0.84[EUR][1000 genomes]
rs2516832	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516833	0.84[EUR][1000 genomes]
rs2516834	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516835	0.85[EUR][1000 genomes]
rs2516836	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2632260	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632261	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2632277	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632283	0.85[EUR][1000 genomes]
rs2632284	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964969	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2969379	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34252185	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34272114	0.87[EUR][1000 genomes]
rs34766932	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35461437	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36071868	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4340581	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4347885	0.82[EUR][1000 genomes]
rs4402818	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4588238	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4622780	0.90[ASN][1000 genomes]
rs4850897	0.84[EUR][1000 genomes]
rs4851187	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851188	0.85[EUR][1000 genomes]
rs6542852	0.87[ASN][1000 genomes]
rs6542858	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6542864	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542865	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542866	0.85[EUR][1000 genomes]
rs6542868	0.84[EUR][1000 genomes]
rs6542869	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542870	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704766	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6708576	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6708878	0.84[EUR][1000 genomes]
rs6712704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6717723	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6717729	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726618	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6727749	0.84[EUR][1000 genomes]
rs6736064	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6739579	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741773	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6743355	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751927	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6753063	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6753650	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6756650	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6757661	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759354	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs720228	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs720229	0.86[EUR][1000 genomes]
rs7349217	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558004	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558239	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7572660	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7577477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7604557	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7605843	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7608938	0.84[EUR][1000 genomes]
rs8179690	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs896886	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9308816	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs972768	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9808541	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9941561	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6542863	TSGA10	cis	lung	GTEx
rs6542863	MITD1	cis	Esophagus Mucosa	GTEx
rs6542863	TSGA10	cis	Esophagus Mucosa	GTEx
rs6542863	MITD1	cis	Nerve Tibial	GTEx
rs6542863	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs6542863	TSGA10	cis	Thyroid	GTEx
rs6542863	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6542863	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs6542863	TSGA10	cis	multi-tissue	Pritchard
rs6542863	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99718000-99740200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:99718200-99729400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:99718600-99739600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:99718800-99727200	Weak transcription	Primary T cells from cord blood	blood
5	chr2:99723800-99739600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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