Variant report

Variant	rs11895749
Chromosome Location	chr2:99746290-99746291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99740982..99744069-chr2:99744600..99746816,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135951	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10167390	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10170063	0.91[ASN][1000 genomes]
rs10181422	0.81[ASN][1000 genomes]
rs1044575	0.84[EUR][1000 genomes]
rs10865029	0.87[EUR][1000 genomes]
rs11123761	0.86[EUR][1000 genomes]
rs11123762	0.87[EUR][1000 genomes]
rs11123763	0.87[EUR][1000 genomes]
rs11123764	0.87[EUR][1000 genomes]
rs11123765	0.91[EUR][1000 genomes]
rs11123766	0.84[EUR][1000 genomes]
rs11123770	0.94[EUR][1000 genomes]
rs1115756	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1115757	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1133977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133978	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674894	0.91[EUR][1000 genomes]
rs11677247	0.85[EUR][1000 genomes]
rs11678456	0.86[EUR][1000 genomes]
rs11683107	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11683188	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685759	0.90[EUR][1000 genomes]
rs11688004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689265	0.89[EUR][1000 genomes]
rs11692336	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692669	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692699	0.87[EUR][1000 genomes]
rs11693427	0.83[EUR][1000 genomes]
rs11695379	0.87[EUR][1000 genomes]
rs11695751	0.92[EUR][1000 genomes]
rs11883676	0.84[EUR][1000 genomes]
rs11890338	0.85[EUR][1000 genomes]
rs11900670	0.87[EUR][1000 genomes]
rs11903311	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12470471	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12613624	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619780	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621007	0.89[EUR][1000 genomes]
rs12987548	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12991189	0.89[EUR][1000 genomes]
rs12992218	0.85[EUR][1000 genomes]
rs12992930	0.84[EUR][1000 genomes]
rs12995473	0.85[EUR][1000 genomes]
rs12999417	0.81[EUR][1000 genomes]
rs13000731	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13004491	0.84[EUR][1000 genomes]
rs13008171	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009147	0.82[EUR][1000 genomes]
rs13012481	0.84[EUR][1000 genomes]
rs13018891	0.85[EUR][1000 genomes]
rs13020339	0.82[EUR][1000 genomes]
rs13022329	0.87[EUR][1000 genomes]
rs13023501	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13023744	0.92[EUR][1000 genomes]
rs13026928	0.85[EUR][1000 genomes]
rs13030961	0.89[EUR][1000 genomes]
rs13031919	0.88[EUR][1000 genomes]
rs13033012	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13035311	0.86[EUR][1000 genomes]
rs13035357	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407840	0.83[ASN][1000 genomes]
rs13798	0.84[EUR][1000 genomes]
rs1453563	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453564	0.82[ASN][1000 genomes]
rs1563106	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1563107	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1563108	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17708262	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17759607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084988	0.89[ASN][1000 genomes]
rs2171359	0.84[EUR][1000 genomes]
rs2171362	0.81[EUR][1000 genomes]
rs2309581	0.84[EUR][1000 genomes]
rs2516827	0.85[EUR][1000 genomes]
rs2516828	0.85[EUR][1000 genomes]
rs2516829	0.85[EUR][1000 genomes]
rs2516830	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516832	0.85[EUR][1000 genomes]
rs2516833	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516834	0.88[EUR][1000 genomes]
rs2516835	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516836	0.83[EUR][1000 genomes]
rs2632260	0.91[EUR][1000 genomes]
rs2632261	0.85[EUR][1000 genomes]
rs2632277	0.91[EUR][1000 genomes]
rs2632283	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2632284	0.88[EUR][1000 genomes]
rs28648058	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2964969	0.84[EUR][1000 genomes]
rs2969379	0.91[EUR][1000 genomes]
rs34252185	0.92[EUR][1000 genomes]
rs34272114	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34766932	0.85[EUR][1000 genomes]
rs36071868	0.92[EUR][1000 genomes]
rs4340581	0.91[EUR][1000 genomes]
rs4347885	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4402818	0.86[EUR][1000 genomes]
rs4588238	0.86[EUR][1000 genomes]
rs4850897	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851183	0.88[ASN][1000 genomes]
rs4851187	0.92[EUR][1000 genomes]
rs4851188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62154638	0.91[ASN][1000 genomes]
rs6542846	0.82[ASN][1000 genomes]
rs6542863	0.87[EUR][1000 genomes]
rs6542864	0.87[EUR][1000 genomes]
rs6542865	0.85[EUR][1000 genomes]
rs6542866	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542868	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542869	0.84[EUR][1000 genomes]
rs6542870	0.84[EUR][1000 genomes]
rs6707462	0.86[ASN][1000 genomes]
rs6708576	0.84[EUR][1000 genomes]
rs6708878	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6712704	0.87[EUR][1000 genomes]
rs6717723	0.89[EUR][1000 genomes]
rs6717729	0.84[EUR][1000 genomes]
rs6722164	0.81[ASN][1000 genomes]
rs6724476	0.88[ASN][1000 genomes]
rs6727749	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6735801	0.91[ASN][1000 genomes]
rs6737257	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6739579	0.87[EUR][1000 genomes]
rs6740054	0.83[ASN][1000 genomes]
rs6741773	0.80[EUR][1000 genomes]
rs6743355	0.87[EUR][1000 genomes]
rs6751927	0.93[EUR][1000 genomes]
rs6753063	0.84[EUR][1000 genomes]
rs6753650	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6754843	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6756650	0.84[EUR][1000 genomes]
rs6757661	0.84[EUR][1000 genomes]
rs720228	0.92[EUR][1000 genomes]
rs720229	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7349217	0.82[EUR][1000 genomes]
rs7558004	0.84[EUR][1000 genomes]
rs7570657	0.91[ASN][1000 genomes]
rs7571390	0.88[ASN][1000 genomes]
rs7572660	0.84[EUR][1000 genomes]
rs7577477	0.87[EUR][1000 genomes]
rs7584809	0.87[EUR][1000 genomes]
rs7586608	0.81[ASN][1000 genomes]
rs7588059	0.82[ASN][1000 genomes]
rs7591794	0.83[ASN][1000 genomes]
rs7604557	0.93[EUR][1000 genomes]
rs7605734	0.90[ASN][1000 genomes]
rs7605843	0.84[EUR][1000 genomes]
rs7606635	0.90[ASN][1000 genomes]
rs7608938	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8179690	0.84[EUR][1000 genomes]
rs9941561	0.85[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	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
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11895749	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs11895749	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs11895749	TSGA10	cis	lung	GTEx
rs11895749	TSGA10	cis	Esophagus Mucosa	GTEx
rs11895749	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11895749	TSGA10	cis	Thyroid	GTEx
rs11895749	TSGA10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99741800-99746800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:99742800-99757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:99743200-99757000	Weak transcription	Small Intestine	intestine
4	chr2:99743400-99756400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:99743400-99756600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:99743400-99756800	Weak transcription	Brain Cingulate Gyrus	brain

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