Variant report

Variant	rs2411308
Chromosome Location	chr15:39954939-39954940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39926150..39927736-chr15:39954644..39957261,2	MCF-7	breast:
2	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
3	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
4	chr15:39945408..39946992-chr15:39953107..39955288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs11070223	0.81[EUR][1000 genomes]
rs11070225	0.81[EUR][1000 genomes]
rs11070226	0.89[EUR][1000 genomes]
rs11070227	0.89[EUR][1000 genomes]
rs11070228	0.89[EUR][1000 genomes]
rs11070231	0.84[ASN][1000 genomes]
rs11630406	0.89[EUR][1000 genomes]
rs11631820	0.94[ASN][1000 genomes]
rs11631824	0.94[ASN][1000 genomes]
rs11632117	0.87[EUR][1000 genomes]
rs11632879	0.87[EUR][1000 genomes]
rs11635103	0.89[EUR][1000 genomes]
rs11636823	0.89[EUR][1000 genomes]
rs11638041	0.87[EUR][1000 genomes]
rs11638558	0.87[EUR][1000 genomes]
rs11852591	0.89[EUR][1000 genomes]
rs11852649	0.89[EUR][1000 genomes]
rs11855487	0.85[EUR][1000 genomes]
rs11856971	0.89[EUR][1000 genomes]
rs12050804	0.94[ASN][1000 genomes]
rs12899323	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12900024	0.84[ASN][1000 genomes]
rs12900583	0.94[ASN][1000 genomes]
rs12901142	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903514	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12908846	0.81[EUR][1000 genomes]
rs12911549	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911999	0.86[ASN][1000 genomes]
rs16969386	0.81[EUR][1000 genomes]
rs16969395	0.81[EUR][1000 genomes]
rs16969426	0.87[EUR][1000 genomes]
rs16969429	0.87[EUR][1000 genomes]
rs16969451	0.87[EUR][1000 genomes]
rs16969459	0.87[EUR][1000 genomes]
rs16969475	0.89[EUR][1000 genomes]
rs16969478	0.89[EUR][1000 genomes]
rs1876853	0.87[EUR][1000 genomes]
rs1906152	0.85[ASN][1000 genomes]
rs1906155	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1906156	0.87[ASN][1000 genomes]
rs2129459	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2411299	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411300	0.89[ASN][1000 genomes]
rs2411301	0.91[ASN][1000 genomes]
rs2411307	0.90[ASN][1000 genomes]
rs2411309	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411310	0.94[ASN][1000 genomes]
rs2411311	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2411312	0.82[AMR][1000 genomes]
rs2411313	0.89[EUR][1000 genomes]
rs2411314	0.89[EUR][1000 genomes]
rs2412413	0.87[EUR][1000 genomes]
rs2412414	0.87[EUR][1000 genomes]
rs2412415	0.87[EUR][1000 genomes]
rs2412416	0.87[EUR][1000 genomes]
rs2412417	0.87[EUR][1000 genomes]
rs2631697	0.87[ASN][1000 genomes]
rs2631700	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2631701	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2631702	0.86[ASN][1000 genomes]
rs2631704	0.87[ASN][1000 genomes]
rs2631705	0.87[ASN][1000 genomes]
rs2631710	0.87[ASN][1000 genomes]
rs2664125	0.87[ASN][1000 genomes]
rs2664133	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2664135	0.84[ASN][1000 genomes]
rs28437905	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28581473	0.93[ASN][1000 genomes]
rs2898685	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898686	0.86[EUR][1000 genomes]
rs2898688	0.87[EUR][1000 genomes]
rs2898962	0.87[EUR][1000 genomes]
rs4319738	0.94[ASN][1000 genomes]
rs4349120	0.87[EUR][1000 genomes]
rs4429263	0.89[ASN][1000 genomes]
rs4476148	0.88[ASN][1000 genomes]
rs4479205	0.85[EUR][1000 genomes]
rs4480779	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4493017	0.94[ASN][1000 genomes]
rs4505280	0.94[ASN][1000 genomes]
rs4526992	0.91[EUR][1000 genomes]
rs4547308	0.87[EUR][1000 genomes]
rs4572354	0.84[ASN][1000 genomes]
rs4583211	0.91[EUR][1000 genomes]
rs4591113	0.89[ASN][1000 genomes]
rs4606692	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4628934	0.87[EUR][1000 genomes]
rs4924376	0.89[ASN][1000 genomes]
rs4924377	0.87[ASN][1000 genomes]
rs59449051	0.91[EUR][1000 genomes]
rs60164392	0.87[EUR][1000 genomes]
rs60195210	0.87[EUR][1000 genomes]
rs61130460	0.89[EUR][1000 genomes]
rs61439563	0.91[EUR][1000 genomes]
rs61568256	0.89[EUR][1000 genomes]
rs6492909	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492910	0.94[ASN][1000 genomes]
rs6492911	0.92[ASN][1000 genomes]
rs68183224	0.84[ASN][1000 genomes]
rs7162070	0.87[EUR][1000 genomes]
rs7162781	0.89[EUR][1000 genomes]
rs7167100	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167184	0.89[EUR][1000 genomes]
rs7168755	0.87[EUR][1000 genomes]
rs7169478	0.82[EUR][1000 genomes]
rs7169574	0.82[EUR][1000 genomes]
rs7177857	0.84[ASN][1000 genomes]
rs7179608	0.89[EUR][1000 genomes]
rs72725079	0.87[EUR][1000 genomes]
rs72725080	0.87[EUR][1000 genomes]
rs72725084	0.87[EUR][1000 genomes]
rs72725093	0.89[EUR][1000 genomes]
rs72725101	0.89[EUR][1000 genomes]
rs8026916	0.87[EUR][1000 genomes]
rs8029602	0.89[EUR][1000 genomes]
rs8032289	0.87[EUR][1000 genomes]
rs8033902	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034543	0.94[ASN][1000 genomes]
rs8034885	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035354	0.93[ASN][1000 genomes]
rs8036226	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884584	0.91[EUR][1000 genomes]
rs937960	0.88[ASN][1000 genomes]
rs951358	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9672572	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs999393	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:39944800-39955600	Weak transcription	Fetal Lung	lung
3	chr15:39948400-39956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:39949400-39956200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:39950200-39957200	Weak transcription	HSMM	muscle
6	chr15:39950400-39955800	Weak transcription	Hela-S3	cervix
7	chr15:39950400-39957200	Weak transcription	HSMMtube	muscle
8	chr15:39950800-39957800	Weak transcription	HUVEC	blood vessel
9	chr15:39954200-39955800	Weak transcription	NHLF	lung
10	chr15:39954400-39956400	Weak transcription	Fetal Kidney	kidney
11	chr15:39954400-39958200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:39954400-39958200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:39954400-39958200	Weak transcription	NH-A	brain
14	chr15:39954400-39959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:39954600-39958200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:39954800-39956200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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