Variant report

Variant	rs11070264
Chromosome Location	chr15:40611861-40611862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40607352..40610567-chr15:40611377..40615529,4	MCF-7	breast:
2	chr15:40609528..40613420-chr15:40614090..40617606,5	K562	blood:
3	chr15:40329590..40332375-chr15:40611438..40613326,2	K562	blood:

Variant related genes	Relation type
ENSG00000248508	Chromatin interaction
ENSG00000140319	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1077476	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2118961	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2289333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2289334	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4277318	0.94[ASN][1000 genomes]
rs4334271	0.86[JPT][hapmap]
rs4923863	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923864	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924455	0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7164564	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7164747	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs748245	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs882829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs934937	0.86[CHB][hapmap];0.81[JPT][hapmap]

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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv984054	chr15:40603452-40612578	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11070264	C15orf52	cis	cerebellum	SCAN
rs11070264	DISP2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40584200-40614800	Weak transcription	Gastric	stomach
2	chr15:40600000-40614600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:40601200-40612800	Weak transcription	Right Ventricle	heart
4	chr15:40602000-40612600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40602000-40613000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:40602000-40614600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:40602200-40612600	Weak transcription	Spleen	Spleen
8	chr15:40602600-40614600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:40606000-40615200	Weak transcription	Psoas Muscle	Psoas
10	chr15:40606600-40615000	Weak transcription	Colonic Mucosa	Colon
11	chr15:40607200-40613000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:40607400-40612400	Weak transcription	Fetal Heart	heart
13	chr15:40607400-40612600	Weak transcription	Pancreas	Pancrea
14	chr15:40607400-40613000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:40607400-40613000	Weak transcription	Fetal Thymus	thymus
16	chr15:40607400-40614600	Weak transcription	Hela-S3	cervix
17	chr15:40607600-40612600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:40607600-40614600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:40607800-40612200	Weak transcription	HSMMtube	muscle
20	chr15:40607800-40613000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:40607800-40613000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:40607800-40613000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:40607800-40614200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:40607800-40614200	Weak transcription	HMEC	breast
25	chr15:40608000-40613000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:40608000-40614600	Weak transcription	HSMM	muscle
27	chr15:40608000-40615000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:40608200-40612800	Weak transcription	HUVEC	blood vessel
29	chr15:40609400-40614400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:40610600-40614800	Weak transcription	GM12878-XiMat	blood
31	chr15:40610800-40612800	Weak transcription	Primary B cells from cord blood	blood
32	chr15:40610800-40614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:40611800-40612600	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links