Variant report

Variant	rs8041042
Chromosome Location	chr15:52398065-52398066
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	chr15:52395553..52398772-chr15:52399645..52403144,6	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10400852	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953085	1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs7163133	1.00[EUR][1000 genomes]
rs7164357	1.00[EUR][1000 genomes]
rs7165157	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	1.00[EUR][1000 genomes]
rs73402803	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402824	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402826	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	1.00[EUR][1000 genomes]
rs73402853	1.00[EUR][1000 genomes]
rs73402859	1.00[EUR][1000 genomes]
rs73402869	1.00[EUR][1000 genomes]
rs73402879	1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	1.00[EUR][1000 genomes]
rs8035146	1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041128	1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52386200-52399000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52392200-52400800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:52392400-52398600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:52392600-52398600	Enhancers	HMEC	breast
5	chr15:52392600-52398600	Enhancers	NHEK	skin
6	chr15:52393200-52401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:52393200-52401800	Weak transcription	Pancreas	Pancrea
8	chr15:52393400-52398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:52395800-52398200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:52395800-52401200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:52396000-52401000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:52396000-52401800	Weak transcription	HSMM	muscle
13	chr15:52396800-52399000	Weak transcription	Spleen	Spleen
14	chr15:52396800-52401000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:52397000-52398200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:52397000-52398800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:52397000-52398800	Weak transcription	Hela-S3	cervix
18	chr15:52397000-52399000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:52397000-52401000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:52397000-52401000	Weak transcription	Adipose Nuclei	Adipose
21	chr15:52397000-52401000	Enhancers	GM12878-XiMat	blood
22	chr15:52397400-52401800	Weak transcription	Primary B cells from cord blood	blood
23	chr15:52397600-52398600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:52397800-52398400	Enhancers	Brain Angular Gyrus	brain
25	chr15:52397800-52398400	Enhancers	Brain Hippocampus Middle	brain
26	chr15:52397800-52398600	Enhancers	Brain Substantia Nigra	brain
27	chr15:52397800-52399000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr15:52397800-52399400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:52398000-52398200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:52398000-52398600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:52398000-52398600	Enhancers	Brain Cingulate Gyrus	brain
32	chr15:52398000-52398600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr15:52398000-52399400	Enhancers	HepG2	liver

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