Variant report

Variant	rs11854876
Chromosome Location	chr15:74251305-74251306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74217751..74219998-chr15:74250124..74252297,2	MCF-7	breast:
2	chr15:74245232..74249723-chr15:74250188..74253151,4	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
ENSG00000129038	Chromatin interaction
ENSG00000261801	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10152126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152898	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10152975	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1078555	0.90[CHB][hapmap]
rs11072453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072455	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072456	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11072457	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11630778	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636435	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11858082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050565	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12102019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438442	0.85[YRI][hapmap]
rs12898704	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12906079	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12907105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907194	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12907609	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12913399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12917449	0.80[CHB][hapmap];0.93[GIH][hapmap]
rs1550434	0.90[CHB][hapmap]
rs28405144	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28642047	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34080912	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9630437	0.86[AFR][1000 genomes];0.91[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11854876	STOML1	cis	cerebellum	SCAN
rs11854876	UBL7	cis	cerebellum	SCAN
rs11854876	CYP11A1	cis	cerebellum	SCAN
rs11854876	BBS4	cis	parietal	SCAN
rs11854876	LRRC49	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74245400-74257400	Weak transcription	Fetal Lung	lung
2	chr15:74246000-74252400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:74247800-74253000	Enhancers	Primary hematopoietic stem cells	blood
4	chr15:74248000-74251800	Enhancers	Osteobl	bone
5	chr15:74248000-74252400	Enhancers	NH-A	brain
6	chr15:74248200-74252600	Enhancers	HSMMtube	muscle
7	chr15:74248200-74254200	Enhancers	Fetal Thymus	thymus
8	chr15:74248200-74257200	Weak transcription	Right Ventricle	heart
9	chr15:74248400-74253800	Enhancers	Thymus	Thymus
10	chr15:74249200-74252600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:74249400-74251400	Enhancers	Primary T cells from cord blood	blood
12	chr15:74249400-74251400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:74249400-74251600	Weak transcription	Small Intestine	intestine
14	chr15:74249400-74252400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:74249400-74254200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:74249400-74257400	Weak transcription	Adipose Nuclei	Adipose
17	chr15:74249600-74251400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:74249600-74252400	Enhancers	HMEC	breast
19	chr15:74249600-74252600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:74249800-74252400	Enhancers	HSMM	muscle
21	chr15:74249800-74253000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr15:74249800-74255000	Weak transcription	HUVEC	blood vessel
23	chr15:74249800-74257400	Weak transcription	A549	lung
24	chr15:74250000-74251400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:74250000-74251400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:74250000-74251600	Weak transcription	Spleen	Spleen
27	chr15:74250000-74252200	Weak transcription	Placenta	Placenta
28	chr15:74250000-74257200	Weak transcription	Gastric	stomach
29	chr15:74250200-74257400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:74250400-74251400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:74250400-74251400	Weak transcription	NHDF-Ad	bronchial
32	chr15:74250400-74252000	Enhancers	Stomach Mucosa	stomach
33	chr15:74250400-74252400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr15:74250600-74253400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr15:74250800-74251400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:74250800-74251400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr15:74250800-74251800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr15:74250800-74252400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:74250800-74252800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:74251000-74252000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:74251000-74252000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:74251000-74252400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:74251000-74252400	Enhancers	Fetal Muscle Leg	muscle
44	chr15:74251000-74252400	Enhancers	NHLF	lung
45	chr15:74251000-74253000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr15:74251200-74251400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:74251200-74251800	Enhancers	Duodenum Mucosa	Duodenum
48	chr15:74251200-74251800	Enhancers	Hela-S3	cervix
49	chr15:74251200-74252000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr15:74251200-74252000	Flanking Active TSS	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links