Variant report

Variant	rs12467679
Chromosome Location	chr2:99654449-99654450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99345574..99348199-chr2:99652477..99654603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10153626	0.85[AMR][1000 genomes]
rs10165534	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170063	0.85[EUR][1000 genomes]
rs10179043	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10181422	0.81[EUR][1000 genomes]
rs10193019	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10193113	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10196680	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202452	0.97[EUR][1000 genomes]
rs1044575	0.82[ASN][1000 genomes]
rs10865029	0.97[ASN][1000 genomes]
rs11123761	0.97[ASN][1000 genomes]
rs11123762	0.90[ASN][1000 genomes]
rs11123763	0.87[ASN][1000 genomes]
rs11123764	0.87[ASN][1000 genomes]
rs11123765	0.85[ASN][1000 genomes]
rs11123766	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1115756	0.83[EUR][1000 genomes]
rs1115757	0.83[EUR][1000 genomes]
rs11677247	0.87[ASN][1000 genomes]
rs11677321	0.82[ASN][1000 genomes]
rs11678456	0.97[ASN][1000 genomes]
rs11685759	0.85[ASN][1000 genomes]
rs11689265	0.81[ASN][1000 genomes]
rs11692699	0.90[ASN][1000 genomes]
rs11693427	0.81[ASN][1000 genomes]
rs11695379	0.88[ASN][1000 genomes]
rs11695751	0.95[ASN][1000 genomes]
rs11883676	0.82[ASN][1000 genomes]
rs11890338	0.84[ASN][1000 genomes]
rs11900670	0.97[ASN][1000 genomes]
rs12464710	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12470471	0.81[EUR][1000 genomes]
rs12473029	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475034	0.82[EUR][1000 genomes]
rs12477754	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477978	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621007	0.81[ASN][1000 genomes]
rs12992218	0.87[ASN][1000 genomes]
rs12995473	0.87[ASN][1000 genomes]
rs13004491	0.87[ASN][1000 genomes]
rs13008496	0.83[ASN][1000 genomes]
rs13009147	0.81[ASN][1000 genomes]
rs13018891	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13020339	0.85[ASN][1000 genomes]
rs13022329	0.87[ASN][1000 genomes]
rs13023744	0.88[ASN][1000 genomes]
rs13030961	0.81[ASN][1000 genomes]
rs13035311	0.97[ASN][1000 genomes]
rs13396358	0.97[EUR][1000 genomes]
rs13407840	0.83[EUR][1000 genomes]
rs13412640	0.90[AMR][1000 genomes]
rs13412764	0.95[EUR][1000 genomes]
rs1349778	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349779	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13798	0.82[ASN][1000 genomes]
rs1453564	0.83[EUR][1000 genomes]
rs1530996	0.89[EUR][1000 genomes]
rs1580068	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17708218	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17708262	0.81[EUR][1000 genomes]
rs1993230	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2045057	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2084988	0.85[EUR][1000 genomes]
rs2171359	0.82[ASN][1000 genomes]
rs2309524	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309581	0.85[ASN][1000 genomes]
rs2516827	0.87[ASN][1000 genomes]
rs2516828	0.87[ASN][1000 genomes]
rs2516829	0.87[ASN][1000 genomes]
rs2516832	0.87[ASN][1000 genomes]
rs2516834	0.85[ASN][1000 genomes]
rs2516836	0.84[ASN][1000 genomes]
rs2632260	0.85[ASN][1000 genomes]
rs2632261	0.87[ASN][1000 genomes]
rs2632277	0.85[ASN][1000 genomes]
rs2632284	0.85[ASN][1000 genomes]
rs28648058	0.81[EUR][1000 genomes]
rs2964969	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2969379	0.85[ASN][1000 genomes]
rs34252185	0.88[ASN][1000 genomes]
rs34766932	0.90[ASN][1000 genomes]
rs35001733	0.95[EUR][1000 genomes]
rs35461437	0.81[ASN][1000 genomes]
rs36071868	0.88[ASN][1000 genomes]
rs4340581	0.88[ASN][1000 genomes]
rs4346439	0.81[AMR][1000 genomes]
rs4402818	0.97[ASN][1000 genomes]
rs4585080	0.80[EUR][1000 genomes]
rs4588238	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4622780	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851179	0.91[EUR][1000 genomes]
rs4851183	0.84[EUR][1000 genomes]
rs4851187	0.88[ASN][1000 genomes]
rs60012524	0.83[EUR][1000 genomes]
rs62154638	0.83[EUR][1000 genomes]
rs62156364	0.85[EUR][1000 genomes]
rs62156558	0.80[EUR][1000 genomes]
rs6542846	0.83[EUR][1000 genomes]
rs6542852	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542858	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542863	0.90[ASN][1000 genomes]
rs6542864	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6542865	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6542869	0.85[ASN][1000 genomes]
rs6542870	0.82[ASN][1000 genomes]
rs6704766	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708576	0.82[ASN][1000 genomes]
rs6712704	0.97[ASN][1000 genomes]
rs6717723	0.85[ASN][1000 genomes]
rs6717729	0.87[ASN][1000 genomes]
rs6721535	0.95[EUR][1000 genomes]
rs6722164	0.81[EUR][1000 genomes]
rs6724476	0.84[EUR][1000 genomes]
rs6726618	0.81[ASN][1000 genomes]
rs6732579	0.95[EUR][1000 genomes]
rs6735801	0.84[EUR][1000 genomes]
rs6736064	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737257	0.81[EUR][1000 genomes]
rs6739579	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6740035	0.95[EUR][1000 genomes]
rs6740054	0.83[EUR][1000 genomes]
rs6740267	0.97[EUR][1000 genomes]
rs6741773	0.81[ASN][1000 genomes]
rs6743355	0.90[ASN][1000 genomes]
rs6751927	0.88[ASN][1000 genomes]
rs6753063	0.82[ASN][1000 genomes]
rs6754843	0.81[EUR][1000 genomes]
rs6756650	0.82[ASN][1000 genomes]
rs6757661	0.82[ASN][1000 genomes]
rs6759354	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720228	0.95[ASN][1000 genomes]
rs7349217	0.82[ASN][1000 genomes]
rs7558004	0.82[ASN][1000 genomes]
rs7558239	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7570657	0.83[EUR][1000 genomes]
rs7571390	0.84[EUR][1000 genomes]
rs7572660	0.82[ASN][1000 genomes]
rs7577477	0.90[ASN][1000 genomes]
rs7584809	0.87[ASN][1000 genomes]
rs7586608	0.81[EUR][1000 genomes]
rs7591794	0.83[EUR][1000 genomes]
rs7604557	0.85[ASN][1000 genomes]
rs7605734	0.84[EUR][1000 genomes]
rs7605843	0.82[ASN][1000 genomes]
rs7606635	0.84[EUR][1000 genomes]
rs8179690	0.82[ASN][1000 genomes]
rs896886	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308816	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972768	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9808541	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9941561	0.87[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12467679	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs12467679	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs12467679	TSGA10	cis	Thyroid	GTEx
rs12467679	TSGA10	cis	multi-tissue	Pritchard
rs12467679	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99627600-99658800	Weak transcription	Pancreas	Pancrea
2	chr2:99650000-99656800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:99653400-99657600	Weak transcription	Aorta	Aorta

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