Variant report

Variant	rs6493163
Chromosome Location	chr15:45941689-45941690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45940658..45942644-chr15:45946028..45948330,2	MCF-7	breast:
2	chr15:45936300..45938060-chr15:45941234..45942847,2	MCF-7	breast:
3	chr15:45931592..45934146-chr15:45938709..45942844,4	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12708404	1.00[ASN][1000 genomes]
rs12907319	1.00[ASN][1000 genomes]
rs12910629	1.00[ASN][1000 genomes]
rs12915009	1.00[ASN][1000 genomes]
rs2733249	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35394591	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35707605	1.00[ASN][1000 genomes]
rs7496542	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a
4	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv526945	chr15:45935755-45941689	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493163	C15orf52	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45933800-45951200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:45934200-45961600	Weak transcription	Fetal Kidney	kidney
3	chr15:45934800-45945800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:45936600-45942800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr15:45937200-45945600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr15:45938400-45950400	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:45938600-45942000	Weak transcription	Gastric	stomach
8	chr15:45938600-45942600	Weak transcription	Fetal Stomach	stomach
9	chr15:45938600-45943000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:45938600-45951000	Weak transcription	Primary B cells from cord blood	blood
11	chr15:45938600-45952600	Weak transcription	Adipose Nuclei	Adipose
12	chr15:45938800-45942400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:45938800-45945600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:45938800-45949400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:45938800-45954200	Weak transcription	Aorta	Aorta
16	chr15:45939600-45942800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr15:45939600-45942800	Enhancers	Lung	lung
18	chr15:45939800-45942600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:45940000-45942600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:45940000-45942600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr15:45940000-45942800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:45940000-45942800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:45940000-45942800	Enhancers	Liver	Liver
24	chr15:45940200-45942400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:45940400-45942200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:45940400-45942400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:45940400-45942600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr15:45940400-45943800	Enhancers	Pancreas	Pancrea
29	chr15:45940600-45941800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr15:45940600-45942000	Enhancers	Fetal Intestine Small	intestine
31	chr15:45940600-45942200	Enhancers	NHDF-Ad	bronchial
32	chr15:45940600-45942400	Enhancers	Fetal Intestine Large	intestine
33	chr15:45940600-45942800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr15:45940600-45942800	Enhancers	Stomach Mucosa	stomach
35	chr15:45940600-45942800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr15:45940800-45942200	Enhancers	Esophagus	oesophagus
37	chr15:45940800-45942200	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr15:45940800-45942400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:45940800-45942400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:45940800-45942600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:45940800-45942600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:45940800-45942600	Enhancers	Right Atrium	heart
43	chr15:45940800-45942800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:45940800-45942800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr15:45940800-45942800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr15:45940800-45943000	Enhancers	Colon Smooth Muscle	Colon
47	chr15:45941200-45942200	Enhancers	Osteobl	bone
48	chr15:45941200-45942400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:45941200-45942600	Enhancers	HMEC	breast
50	chr15:45941200-45945600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links