Variant report

Variant	rs745032
Chromosome Location	chr15:41102667-41102668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:
2	chr15:41097893..41103310-chr15:41103796..41109268,7	MCF-7	breast:
3	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
4	chr1:45186004..45188513-chr15:41102404..41103904,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000166145	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10152371	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070294	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070296	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070297	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11856866	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858010	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148058	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12899910	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905621	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12909824	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916485	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12916535	0.86[EUR][1000 genomes]
rs17657877	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17657986	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2010300	0.84[CEU][hapmap];0.83[MEX][hapmap]
rs2289219	0.84[CEU][hapmap]
rs2412567	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2899000	0.84[CEU][hapmap]
rs34143869	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34817886	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34948298	0.91[EUR][1000 genomes]
rs35458726	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35621205	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35853942	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743033	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743034	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4402538	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56886112	0.87[EUR][1000 genomes]
rs57818172	0.87[EUR][1000 genomes]
rs57825040	0.87[EUR][1000 genomes]
rs57943888	0.87[EUR][1000 genomes]
rs57994257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62018585	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6492967	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8036842	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8037830	0.88[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs745032	ZFYVE19	cis	cerebellum	SCAN
rs745032	C15orf23	cis	cerebellum	SCAN
rs745032	C15orf57	cis	cerebellum	SCAN
rs745032	ZFYVE19	cis	Thyroid	GTEx
rs745032	ZFYVE19	cis	Artery Tibial	GTEx
rs745032	C15orf57	cis	lymphoblastoid	seeQTL
rs745032	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs745032	C15orf57	cis	Adipose Subcutaneous	GTEx
rs745032	RP11-111A22.1	cis	Artery Tibial	GTEx
rs745032	C15orf57	cis	Artery Tibial	GTEx
rs745032	ZFYVE19	cis	parietal	SCAN
rs745032	ZFYVE19	cis	lymphoblastoid	seeQTL
rs745032	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs745032	THBS1	cis	cerebellum	SCAN
rs745032	ZFYVE19	cis	multi-tissue	Pritchard
rs745032	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs745032	ZFYVE19	cis	Nerve Tibial	GTEx
rs745032	CCDC32	cis	multi-tissue	Pritchard
rs745032	C15orf57	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41100200-41107600	Weak transcription	Aorta	Aorta
2	chr15:41100400-41107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:41100600-41102800	Weak transcription	HSMMtube	muscle
4	chr15:41100600-41103000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:41100600-41103000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:41100600-41103400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:41100600-41103800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:41100600-41104600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:41100600-41107800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:41100600-41108800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:41100600-41108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:41100800-41102800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:41100800-41102800	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:41100800-41102800	Weak transcription	HUVEC	blood vessel
15	chr15:41100800-41102800	Weak transcription	Osteobl	bone
16	chr15:41100800-41103000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:41100800-41103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:41100800-41103000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:41100800-41103200	Weak transcription	Primary B cells from cord blood	blood
20	chr15:41100800-41103200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:41100800-41104200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:41100800-41105200	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:41100800-41106000	Weak transcription	NH-A	brain
24	chr15:41100800-41107000	Weak transcription	Fetal Kidney	kidney
25	chr15:41100800-41107400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:41100800-41107600	Weak transcription	Fetal Brain Male	brain
27	chr15:41100800-41109200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:41100800-41120200	Weak transcription	Small Intestine	intestine
29	chr15:41101000-41102800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:41101000-41103000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:41101000-41103000	Weak transcription	NHDF-Ad	bronchial
32	chr15:41101000-41104800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:41101000-41107400	Weak transcription	Stomach Mucosa	stomach
34	chr15:41101200-41102800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:41101200-41107200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:41101200-41107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:41101200-41110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:41101400-41102800	Genic enhancers	Duodenum Mucosa	Duodenum
39	chr15:41101400-41103000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:41101400-41103200	Strong transcription	Esophagus	oesophagus
41	chr15:41101400-41103200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:41101400-41105000	Strong transcription	Placenta	Placenta
43	chr15:41101400-41105600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr15:41101400-41106800	Strong transcription	Gastric	stomach
45	chr15:41101400-41107000	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:41101400-41107400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr15:41101400-41107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:41101400-41107800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:41101400-41109200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:41101400-41109600	Strong transcription	Fetal Intestine Small	intestine

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