Variant report

Variant	rs12910589
Chromosome Location	chr15:42392483-42392484
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42384743..42386720-chr15:42391434..42393196,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11629612	0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2003956	0.92[CHD][hapmap];0.82[JPT][hapmap]
rs627836	0.83[ASN][1000 genomes]
rs645178	0.83[ASN][1000 genomes]
rs72537460	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs776721	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028204	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8028379	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs811850	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12910589	RTF1	cis	parietal	SCAN
rs12910589	C15orf53	cis	cerebellum	SCAN
rs12910589	BMF	cis	cerebellum	SCAN
rs12910589	WDR76	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42386000-42397600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:42386800-42392600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:42386800-42392600	Weak transcription	Pancreas	Pancrea
4	chr15:42387200-42392600	Weak transcription	Esophagus	oesophagus
5	chr15:42389600-42396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:42391200-42392600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:42391600-42393600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr15:42391800-42393000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:42391800-42393000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:42392000-42393000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:42392000-42393200	Enhancers	Primary hematopoietic stem cells	blood
12	chr15:42392000-42393200	Enhancers	HUVEC	blood vessel
13	chr15:42392000-42393200	Enhancers	NHEK	skin
14	chr15:42392000-42393400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr15:42392200-42392600	Enhancers	Brain Hippocampus Middle	brain
16	chr15:42392200-42392800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:42392200-42393000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:42392200-42393000	Enhancers	HMEC	breast
19	chr15:42392200-42393200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr15:42392200-42393200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:42392200-42393200	Enhancers	Placenta	Placenta
22	chr15:42392200-42393200	Enhancers	Gastric	stomach
23	chr15:42392200-42393200	Enhancers	Lung	lung
24	chr15:42392200-42393200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr15:42392200-42393200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr15:42392200-42393800	Enhancers	Stomach Mucosa	stomach
27	chr15:42392400-42392800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:42392400-42392800	Flanking Active TSS	HepG2	liver
29	chr15:42392400-42393000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:42392400-42393000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr15:42392400-42393000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr15:42392400-42393000	Enhancers	Duodenum Mucosa	Duodenum
33	chr15:42392400-42393000	Enhancers	Hela-S3	cervix
34	chr15:42392400-42393200	Enhancers	Primary B cells from cord blood	blood
35	chr15:42392400-42393200	Enhancers	Adipose Nuclei	Adipose
36	chr15:42392400-42393200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr15:42392400-42393200	Enhancers	Spleen	Spleen
38	chr15:42392400-42393400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr15:42392400-42395000	Enhancers	NH-A	brain
40	chr15:42392400-42395200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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