Variant report

Variant	rs2010300
Chromosome Location	chr15:41080131-41080132
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41078916..41081260-chr15:41083932..41085617,2	MCF-7	breast:
2	chr15:41074776..41077084-chr15:41079776..41081556,2	K562	blood:
3	chr15:41034636..41037177-chr15:41079294..41081993,2	MCF-7	breast:
4	chr15:41076638..41081333-chr15:41183432..41186983,4	MCF-7	breast:
5	chr15:41079101..41081829-chr15:41185816..41187500,2	MCF-7	breast:
6	chr15:41076760..41081645-chr15:41164224..41167556,4	MCF-7	breast:
7	chr15:41076601..41080762-chr15:41116674..41123009,6	MCF-7	breast:
8	chr15:41073963..41081336-chr15:41133817..41139655,12	MCF-7	breast:
9	chr15:41073204..41083534-chr15:41133992..41141155,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166143	Chromatin interaction
ENSG00000264256	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000104142	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10152371	0.83[MEX][hapmap]
rs1051482	1.00[ASW][hapmap];0.83[CEU][hapmap]
rs11070290	0.86[EUR][1000 genomes]
rs11070295	0.84[CEU][hapmap];0.83[MEX][hapmap]
rs11070296	0.84[CEU][hapmap];0.83[MEX][hapmap]
rs11855641	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148185	0.83[CEU][hapmap]
rs12898552	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12906755	0.81[CEU][hapmap]
rs12907448	0.81[CEU][hapmap]
rs12910784	0.85[EUR][1000 genomes]
rs17657986	0.83[MEX][hapmap]
rs2289219	1.00[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs2304583	0.92[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2412545	0.92[CEU][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs2899000	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34621344	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34988257	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3736286	0.84[CEU][hapmap];0.89[MEX][hapmap]
rs3743033	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs3743034	0.83[MEX][hapmap]
rs3759796	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4457966	0.82[CEU][hapmap]
rs45592734	0.84[EUR][1000 genomes]
rs5030783	0.92[CEU][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs56886112	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57818172	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57825040	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57943888	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62018584	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745032	0.84[CEU][hapmap];0.83[MEX][hapmap]
rs8031427	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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:29)

SNP	Gene	Cis/trans	Tissue	Source
rs2010300	C15orf57	cis	Stomach	GTEx
rs2010300	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs2010300	ZFYVE19	cis	multi-tissue	Pritchard
rs2010300	C15orf57	cis	Artery Aorta	GTEx
rs2010300	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2010300	C15orf57	cis	Artery Tibial	GTEx
rs2010300	ZFYVE19	cis	parietal	SCAN
rs2010300	C15orf57	cis	Esophagus Muscularis	GTEx
rs2010300	C15orf57	cis	cerebellum	SCAN
rs2010300	C15orf57	cis	parietal	SCAN
rs2010300	C15orf57	cis	Esophagus Mucosa	GTEx
rs2010300	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs2010300	RP11-111A22.1	cis	lung	GTEx
rs2010300	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs2010300	IVD	cis	cerebellum	SCAN
rs2010300	ZFYVE19	cis	cerebellum	SCAN
rs2010300	C15orf23	cis	cerebellum	SCAN
rs2010300	C15orf57	cis	Cerebellum	GTEx
rs2010300	C15orf57	cis	lymphoblastoid	seeQTL
rs2010300	RP11-111A22.1	cis	Stomach	GTEx
rs2010300	ZFYVE19	cis	Cerebellum	GTEx
rs2010300	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2010300	C15orf23	cis	parietal	SCAN
rs2010300	C15orf57	cis	lung	GTEx
rs2010300	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2010300	MGC20481	cis	multi-tissue	Pritchard
rs2010300	DISP2	cis	Thyroid	GTEx
rs2010300	C15orf57	cis	Nerve Tibial	GTEx
rs2010300	CCDC32	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41067600-41085400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41068000-41087800	Weak transcription	Fetal Heart	heart
3	chr15:41072400-41083400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:41072400-41090200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:41072600-41081400	Weak transcription	Fetal Muscle Leg	muscle
6	chr15:41072600-41082200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:41072600-41082600	Weak transcription	Primary B cells from cord blood	blood
8	chr15:41072600-41084000	Weak transcription	Brain Germinal Matrix	brain
9	chr15:41072600-41098600	Weak transcription	Fetal Brain Female	brain
10	chr15:41072600-41098600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:41072800-41080200	Weak transcription	Fetal Stomach	stomach
12	chr15:41072800-41084200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:41075600-41081200	Weak transcription	K562	blood
14	chr15:41077400-41082200	Enhancers	Stomach Mucosa	stomach
15	chr15:41077600-41080400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr15:41077600-41080600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:41077600-41080600	Enhancers	Placenta	Placenta
18	chr15:41077600-41081600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:41077600-41081800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr15:41077600-41081800	Enhancers	HMEC	breast
21	chr15:41077800-41080400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr15:41077800-41080600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:41077800-41080600	Enhancers	Gastric	stomach
24	chr15:41077800-41080800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr15:41077800-41081600	Enhancers	Small Intestine	intestine
26	chr15:41077800-41081800	Enhancers	Duodenum Mucosa	Duodenum
27	chr15:41077800-41081800	Enhancers	Pancreas	Pancrea
28	chr15:41077800-41082000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:41077800-41082000	Enhancers	Fetal Lung	lung
30	chr15:41077800-41082800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:41078000-41080600	Enhancers	HSMM	muscle
32	chr15:41078200-41098600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:41078400-41081600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:41078600-41080400	Enhancers	Thymus	Thymus
35	chr15:41078600-41080400	Enhancers	NH-A	brain
36	chr15:41078600-41080600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:41078600-41080800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:41078600-41081800	Enhancers	Colonic Mucosa	Colon
39	chr15:41078600-41082000	Enhancers	Esophagus	oesophagus
40	chr15:41078600-41082000	Enhancers	Dnd41	blood
41	chr15:41078800-41080400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:41078800-41080400	Enhancers	Brain Hippocampus Middle	brain
43	chr15:41078800-41080400	Enhancers	Fetal Intestine Small	intestine
44	chr15:41078800-41080400	Enhancers	Osteobl	bone
45	chr15:41078800-41080600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr15:41078800-41080600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr15:41078800-41081400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr15:41078800-41081400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr15:41078800-41081600	Weak transcription	HepG2	liver
50	chr15:41078800-41081800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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