Variant report

Variant	rs4886809
Chromosome Location	chr15:74258449-74258450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74218602..74222336-chr15:74255703..74258772,3	MCF-7	breast:
2	chr15:74226747..74228446-chr15:74257644..74259264,2	MCF-7	breast:
3	chr15:74246924..74252106-chr15:74256220..74259297,4	MCF-7	breast:
4	chr15:74249498..74251558-chr15:74255585..74258590,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261801	Chromatin interaction
ENSG00000129038	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3784563	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs3825941	1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs60822319	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028206	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886809	STOML1	cis	parietal	SCAN
rs4886809	CPLX3	cis	parietal	SCAN
rs4886809	ISLR2	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74255800-74260600	Weak transcription	HUVEC	blood vessel
2	chr15:74256400-74259400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:74256600-74259400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr15:74256600-74259800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:74257000-74258600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:74257000-74259200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:74257200-74258600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr15:74257200-74258600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr15:74257200-74258600	Flanking Active TSS	Thymus	Thymus
10	chr15:74257200-74258800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr15:74257200-74258800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:74257200-74258800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr15:74257200-74259000	Enhancers	Primary B cells from cord blood	blood
14	chr15:74257200-74259200	Enhancers	Primary hematopoietic stem cells	blood
15	chr15:74257200-74259200	Enhancers	Stomach Mucosa	stomach
16	chr15:74257200-74259400	Enhancers	HMEC	breast
17	chr15:74257200-74259400	Enhancers	NH-A	brain
18	chr15:74257400-74258600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr15:74257400-74258600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:74257400-74258600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:74257400-74259000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:74257400-74259200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr15:74257400-74259200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr15:74257400-74259400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:74257400-74259400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr15:74257400-74259400	Enhancers	HSMMtube	muscle
27	chr15:74257400-74259400	Enhancers	NHDF-Ad	bronchial
28	chr15:74257400-74259600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:74257600-74258600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr15:74257600-74258600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:74257600-74258600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr15:74257600-74259000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr15:74257600-74259200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:74257600-74259400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr15:74257600-74259400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:74257800-74258800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:74257800-74258800	Weak transcription	Spleen	Spleen
38	chr15:74257800-74259200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr15:74257800-74259200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr15:74257800-74259200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:74257800-74259200	Enhancers	HSMM	muscle
42	chr15:74257800-74259400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:74257800-74259400	Enhancers	Duodenum Mucosa	Duodenum
44	chr15:74257800-74259600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:74257800-74259800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr15:74257800-74260800	Enhancers	Fetal Thymus	thymus
47	chr15:74257800-74264400	Weak transcription	Placenta	Placenta
48	chr15:74257800-74265200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:74257800-74265200	Weak transcription	Gastric	stomach
50	chr15:74257800-74265200	Weak transcription	Right Atrium	heart

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