Variant report

Variant	rs28378088
Chromosome Location	chr15:59647950-59647951
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	chr15:59642784..59644444-chr15:59647151..59649563,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12438647	1.00[AMR][1000 genomes]
rs16941344	1.00[AMR][1000 genomes]
rs16941346	1.00[AMR][1000 genomes]
rs1967039	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967040	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2414629	1.00[AMR][1000 genomes]
rs28406496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS 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	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59623200-59662800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:59624600-59650000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:59634800-59662600	Weak transcription	Colonic Mucosa	Colon
4	chr15:59636400-59652800	Weak transcription	HepG2	liver
5	chr15:59637800-59662000	Weak transcription	Right Ventricle	heart
6	chr15:59638600-59653000	Weak transcription	Esophagus	oesophagus
7	chr15:59638600-59654600	Weak transcription	Liver	Liver
8	chr15:59640200-59648000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:59641400-59649000	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:59642600-59659400	Weak transcription	Ovary	ovary
11	chr15:59642800-59651600	Weak transcription	Pancreas	Pancrea
12	chr15:59642800-59653200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:59642800-59658600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:59643000-59653000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:59643000-59653000	Weak transcription	HSMMtube	muscle
16	chr15:59643000-59653200	Weak transcription	NHLF	lung
17	chr15:59643000-59656200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:59643000-59659400	Weak transcription	Fetal Intestine Small	intestine
19	chr15:59643200-59648000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:59643200-59650000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:59643200-59650000	Weak transcription	HSMM	muscle
22	chr15:59643600-59648000	Enhancers	Primary B cells from cord blood	blood
23	chr15:59643600-59658800	Weak transcription	Fetal Intestine Large	intestine
24	chr15:59644000-59648000	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:59644000-59653000	Weak transcription	NHDF-Ad	bronchial
26	chr15:59644400-59653000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:59644600-59649800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:59644800-59648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:59644800-59654400	Weak transcription	Osteobl	bone
30	chr15:59644800-59659400	Weak transcription	Right Atrium	heart
31	chr15:59645000-59649000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:59645000-59652800	Weak transcription	Brain Angular Gyrus	brain
33	chr15:59645200-59649400	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:59645200-59649600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:59645200-59649800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:59645200-59656400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:59645200-59659200	Weak transcription	Fetal Heart	heart
38	chr15:59645200-59662000	Weak transcription	Psoas Muscle	Psoas
39	chr15:59645400-59648200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:59645400-59659200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:59645400-59659400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:59646000-59648200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:59646000-59648400	Flanking Active TSS	GM12878-XiMat	blood
44	chr15:59646000-59648600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:59646000-59649000	Enhancers	A549	lung
46	chr15:59646200-59648000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr15:59646200-59648600	Enhancers	Small Intestine	intestine
48	chr15:59646400-59648400	Enhancers	Brain Substantia Nigra	brain
49	chr15:59646400-59648600	Enhancers	Brain Cingulate Gyrus	brain
50	chr15:59646600-59648000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links