Variant report

Variant	rs10152173
Chromosome Location	chr15:74252408-74252409
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	chr15:74245232..74249723-chr15:74250188..74253151,4	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11072451	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072452	0.83[EUR][1000 genomes]
rs11072453	0.82[CHB][hapmap]
rs11072468	0.92[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs11631102	0.83[EUR][1000 genomes]
rs11636435	0.82[CHB][hapmap]
rs11854876	0.82[CHB][hapmap]
rs11858082	0.82[CHB][hapmap]
rs12101466	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12101479	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12102015	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12102019	0.82[CHB][hapmap]
rs12904518	0.92[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs12907105	0.82[CHB][hapmap]
rs12909197	0.82[EUR][1000 genomes]
rs12913399	0.82[CHB][hapmap]
rs2507	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs3816197	0.92[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap]
rs7171694	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs7182319	0.83[AMR][1000 genomes];0.88[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10152173	LRRC49	cis	parietal	SCAN
rs10152173	STOML1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74245400-74257400	Weak transcription	Fetal Lung	lung
2	chr15:74247800-74253000	Enhancers	Primary hematopoietic stem cells	blood
3	chr15:74248200-74252600	Enhancers	HSMMtube	muscle
4	chr15:74248200-74254200	Enhancers	Fetal Thymus	thymus
5	chr15:74248200-74257200	Weak transcription	Right Ventricle	heart
6	chr15:74248400-74253800	Enhancers	Thymus	Thymus
7	chr15:74249200-74252600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr15:74249400-74254200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:74249400-74257400	Weak transcription	Adipose Nuclei	Adipose
10	chr15:74249600-74252600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:74249800-74253000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr15:74249800-74255000	Weak transcription	HUVEC	blood vessel
13	chr15:74249800-74257400	Weak transcription	A549	lung
14	chr15:74250000-74257200	Weak transcription	Gastric	stomach
15	chr15:74250200-74257400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:74250600-74253400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr15:74250800-74252800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr15:74251000-74253000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr15:74251200-74252600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:74251400-74252600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:74251600-74252600	Enhancers	Fetal Muscle Trunk	muscle
22	chr15:74251800-74252600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:74251800-74252800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr15:74251800-74253000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:74251800-74254600	Weak transcription	Osteobl	bone
26	chr15:74251800-74256400	Weak transcription	Fetal Brain Female	brain
27	chr15:74251800-74257200	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:74252000-74252600	Enhancers	Primary T cells from cord blood	blood
29	chr15:74252000-74253000	Enhancers	Dnd41	blood
30	chr15:74252000-74255200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr15:74252000-74256600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:74252000-74257200	Weak transcription	Stomach Mucosa	stomach
33	chr15:74252200-74252600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr15:74252200-74257200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:74252200-74257200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:74252400-74252800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr15:74252400-74254200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:74252400-74256600	Weak transcription	GM12878-XiMat	blood
39	chr15:74252400-74257000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:74252400-74257000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:74252400-74257000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:74252400-74257000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:74252400-74257000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:74252400-74257200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:74252400-74257200	Weak transcription	Primary B cells from cord blood	blood
46	chr15:74252400-74257200	Weak transcription	Fetal Muscle Leg	muscle
47	chr15:74252400-74257200	Weak transcription	Placenta	Placenta
48	chr15:74252400-74257200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:74252400-74257200	Weak transcription	HMEC	breast
50	chr15:74252400-74257200	Weak transcription	HSMM	muscle

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