Variant report

Variant	rs10520153
Chromosome Location	chr15:40080692-40080693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40078363..40080929-chr15:40268662..40270401,2	MCF-7	breast:
2	chr15:40074604..40078535-chr15:40078976..40081815,4	K562	blood:
3	chr15:39873007..39875919-chr15:40078387..40080697,2	MCF-7	breast:
4	chr15:40080053..40082265-chr15:40095277..40098030,2	K562	blood:
5	chr15:40074241..40077863-chr15:40078792..40081577,3	K562	blood:
6	chr15:40078993..40080916-chr15:40082332..40084803,2	K562	blood:
7	chr15:40077135..40079271-chr15:40079393..40081898,2	MCF-7	breast:
8	chr15:40079175..40081149-chr15:40487705..40489916,2	K562	blood:
9	chr15:40079616..40081118-chr15:40086313..40088294,2	MCF-7	breast:
10	chr15:40079722..40082305-chr15:40603620..40606001,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261136	Chromatin interaction
ENSG00000244705	Chromatin interaction
ENSG00000259198	Chromatin interaction
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10520151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12899969	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12903306	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12907894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12916159	0.85[ASN][1000 genomes]
rs17643920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1872762	0.95[EUR][1000 genomes]
rs2171311	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2576930	1.00[JPT][hapmap]
rs2576931	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34185057	1.00[ASN][1000 genomes]
rs34937456	0.85[ASN][1000 genomes]
rs594863	0.89[CEU][hapmap]
rs606927	0.89[CEU][hapmap]
rs62004778	0.85[ASN][1000 genomes]
rs620407	0.89[CEU][hapmap]
rs6492919	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	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
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10520153	RPAP1	cis	parietal	SCAN
rs10520153	DLL4	cis	parietal	SCAN
rs10520153	C15orf54	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40076000-40081000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
3	chr15:40076200-40080800	Weak transcription	Primary B cells from cord blood	blood
4	chr15:40076200-40081400	Weak transcription	Fetal Kidney	kidney
5	chr15:40076600-40081600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:40076600-40082000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:40076600-40082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:40076600-40082600	Weak transcription	Primary T cells from cord blood	blood
9	chr15:40076600-40084200	Weak transcription	Adipose Nuclei	Adipose
10	chr15:40076600-40086200	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:40076600-40090200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:40076600-40092600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:40076800-40082200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr15:40076800-40082400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:40077200-40081200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:40077200-40082600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:40077200-40082600	Enhancers	NHLF	lung
18	chr15:40077200-40092600	Weak transcription	NHEK	skin
19	chr15:40077200-40093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:40077400-40082600	Enhancers	Osteobl	bone
21	chr15:40077600-40082400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr15:40077600-40094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:40077800-40081200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:40077800-40082600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr15:40078000-40082000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr15:40078200-40081200	Enhancers	HSMM	muscle
27	chr15:40078200-40081400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr15:40078200-40082400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr15:40078600-40081200	Enhancers	GM12878-XiMat	blood
30	chr15:40078600-40081600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:40078600-40082400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:40078600-40082400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:40078800-40081000	Weak transcription	K562	blood
34	chr15:40078800-40081400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr15:40078800-40082000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:40078800-40082600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr15:40078800-40082600	Enhancers	NHDF-Ad	bronchial
38	chr15:40079000-40082800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:40079200-40081200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:40079200-40081200	Enhancers	H9 Cell Line	embryonic stem cell
41	chr15:40079200-40081400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:40079400-40080800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:40079400-40081200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:40079400-40082200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr15:40079600-40082600	Enhancers	Fetal Lung	lung
46	chr15:40079800-40081000	Enhancers	HSMMtube	muscle
47	chr15:40079800-40081200	Enhancers	Fetal Thymus	thymus
48	chr15:40080000-40080800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:40080000-40081000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:40080000-40081200	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links