Variant report

Variant	rs17657986
Chromosome Location	chr15:41107415-41107416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41106395..41107951-chr15:41148998..41150842,2	K562	blood:
2	chr15:41097893..41103310-chr15:41103796..41109268,7	MCF-7	breast:
3	chr15:41107252..41108944-chr15:41109410..41111442,2	MCF-7	breast:
4	chr15:41106243..41108618-chr15:41116351..41118366,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166140	Chromatin interaction
ENSG00000104129	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10152371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070294	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070295	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070296	0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856866	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858010	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12148058	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899910	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12909824	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12916485	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916535	0.95[EUR][1000 genomes]
rs17657877	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2010300	0.83[MEX][hapmap]
rs2412567	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs34143869	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34817886	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34948298	0.83[EUR][1000 genomes]
rs35458726	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35621205	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35853942	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736286	0.88[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743033	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402538	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57994257	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62018585	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6492967	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745032	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]
rs8036842	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8037830	0.85[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[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	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
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs17657986	OIP5	cis	parietal	SCAN
rs17657986	C15orf57	cis	Artery Tibial	GTEx
rs17657986	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs17657986	ZFYVE19	cis	Thyroid	GTEx
rs17657986	C15orf57	cis	cerebellum	SCAN
rs17657986	ZFYVE19	cis	Nerve Tibial	GTEx
rs17657986	ZFYVE19	cis	lymphoblastoid	seeQTL
rs17657986	ZFYVE19	cis	Artery Tibial	GTEx
rs17657986	ZFYVE19	cis	Artery Aorta	GTEx
rs17657986	C15orf57	cis	lymphoblastoid	seeQTL
rs17657986	THBS1	cis	cerebellum	SCAN
rs17657986	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs17657986	ZFYVE19	cis	cerebellum	SCAN
rs17657986	ZFYVE19	cis	parietal	SCAN
rs17657986	RP11-111A22.1	cis	Artery Tibial	GTEx
rs17657986	CCDC32	cis	multi-tissue	Pritchard
rs17657986	ZFYVE19	cis	multi-tissue	Pritchard
rs17657986	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs17657986	C15orf57	cis	parietal	SCAN

Chromatin state (count:110 , 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	chr15:41100600-41107800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41100600-41108800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:41100600-41108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:41100800-41107600	Weak transcription	Fetal Brain Male	brain
7	chr15:41100800-41109200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:41100800-41120200	Weak transcription	Small Intestine	intestine
9	chr15:41101200-41110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:41101400-41107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:41101400-41107800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:41101400-41109200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:41101400-41109600	Strong transcription	Fetal Intestine Small	intestine
14	chr15:41101400-41115800	Weak transcription	A549	lung
15	chr15:41101600-41107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:41101600-41107800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:41101600-41107800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr15:41101800-41107800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:41101800-41107800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:41101800-41108000	Strong transcription	Primary T cells from cord blood	blood
21	chr15:41101800-41108200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:41101800-41108400	Strong transcription	Thymus	Thymus
23	chr15:41102000-41107600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr15:41102000-41107800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr15:41102000-41108000	Strong transcription	Fetal Thymus	thymus
26	chr15:41102000-41108200	Strong transcription	Spleen	Spleen
27	chr15:41102000-41108400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr15:41102200-41107800	Strong transcription	Adipose Nuclei	Adipose
29	chr15:41102200-41107800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:41102400-41107600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:41102400-41107600	Strong transcription	Liver	Liver
32	chr15:41102400-41107600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:41102400-41107800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:41102600-41108000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:41102800-41109000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr15:41103200-41108000	Strong transcription	Primary B cells from cord blood	blood
37	chr15:41103400-41107800	Weak transcription	HUVEC	blood vessel
38	chr15:41103400-41110400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:41103600-41108200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:41103600-41109000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:41103800-41107800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr15:41103800-41109000	Weak transcription	GM12878-XiMat	blood
43	chr15:41103800-41115600	Weak transcription	HepG2	liver
44	chr15:41104200-41115800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:41104600-41107800	Strong transcription	NHEK	skin
46	chr15:41104600-41109000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:41104600-41115800	Weak transcription	HMEC	breast
48	chr15:41104800-41107600	Strong transcription	Esophagus	oesophagus
49	chr15:41104800-41108200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:41104800-41108600	Strong transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links