Variant report

Variant	rs10518679
Chromosome Location	chr15:40382441-40382442
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	chr15:40359906..40361762-chr15:40381062..40383010,2	MCF-7	breast:
2	chr15:40370699..40372317-chr15:40379969..40382959,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259584	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12050884	1.00[CHB][hapmap]
rs12913170	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs17723097	1.00[CHB][hapmap]
rs41500744	1.00[ASN][1000 genomes]
rs72731425	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10518679	SRP14-AS1	cis	lung	GTEx
rs10518679	SRP14	cis	parietal	SCAN
rs10518679	AVEN	cis	cerebellum	SCAN
rs10518679	SPRED1	cis	parietal	SCAN
rs10518679	MEIS2	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40374200-40388200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:40374800-40383800	Weak transcription	Brain Substantia Nigra	brain
3	chr15:40375000-40383600	Weak transcription	Brain Anterior Caudate	brain
4	chr15:40375000-40383800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:40375000-40384200	Weak transcription	Brain Angular Gyrus	brain
6	chr15:40376000-40383600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:40377400-40384000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:40378600-40383800	Enhancers	Fetal Heart	heart
9	chr15:40378800-40382600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr15:40378800-40382800	Enhancers	Right Ventricle	heart
11	chr15:40378800-40383000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:40378800-40383000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr15:40378800-40385800	Enhancers	Pancreas	Pancrea
14	chr15:40379000-40384000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:40379400-40384000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr15:40379800-40383000	Enhancers	Left Ventricle	heart
17	chr15:40380000-40384000	Weak transcription	Fetal Brain Male	brain
18	chr15:40380400-40383600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:40380400-40383800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:40380400-40386200	Enhancers	Liver	Liver
21	chr15:40380800-40383000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:40380800-40383600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:40381000-40383400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:40381000-40383800	Weak transcription	Colonic Mucosa	Colon
25	chr15:40381000-40384200	Weak transcription	Esophagus	oesophagus
26	chr15:40381000-40384800	Strong transcription	GM12878-XiMat	blood
27	chr15:40381000-40390200	Genic enhancers	Fetal Stomach	stomach
28	chr15:40381200-40383800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr15:40381200-40384600	Weak transcription	A549	lung
30	chr15:40381200-40384800	Strong transcription	Thymus	Thymus
31	chr15:40381200-40386200	Enhancers	Right Atrium	heart
32	chr15:40381400-40382600	Enhancers	HepG2	liver
33	chr15:40381400-40382800	Weak transcription	Gastric	stomach
34	chr15:40381400-40383000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:40381400-40383400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr15:40381400-40383400	Weak transcription	Brain Germinal Matrix	brain
37	chr15:40381400-40384600	Weak transcription	HSMM	muscle
38	chr15:40381600-40383600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:40381600-40383600	Strong transcription	Primary B cells from cord blood	blood
40	chr15:40381600-40384000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:40381600-40384000	Genic enhancers	Fetal Muscle Leg	muscle
42	chr15:40381600-40384000	Genic enhancers	Placenta	Placenta
43	chr15:40381600-40384000	Strong transcription	Spleen	Spleen
44	chr15:40381600-40386200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:40381600-40386800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:40381800-40383200	Weak transcription	NHDF-Ad	bronchial
47	chr15:40381800-40383400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:40381800-40383400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:40381800-40383600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:40381800-40383600	Genic enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links