Variant report

Variant	rs12148058
Chromosome Location	chr15:41109371-41109372
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41094059..41097035-chr15:41107572..41109488,2	MCF-7	breast:
2	chr15:41107457..41109620-chr15:41136120..41137941,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261183	Chromatin interaction
ENSG00000166145	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10152371	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070294	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070297	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856866	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858010	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12899910	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12905621	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12909824	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12916485	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916535	0.86[EUR][1000 genomes]
rs17657877	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17657986	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34143869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34817886	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34948298	0.91[EUR][1000 genomes]
rs35458726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35621205	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35853942	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736286	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743034	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4402538	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62018585	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492967	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745032	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036842	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037830	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12148058	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs12148058	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12148058	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12148058	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12148058	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12148058	ZFYVE19	cis	Nerve Tibial	GTEx
rs12148058	ZFYVE19	cis	Artery Aorta	GTEx
rs12148058	ZFYVE19	cis	Thyroid	GTEx
rs12148058	ZFYVE19	cis	Artery Tibial	GTEx
rs12148058	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41100800-41120200	Weak transcription	Small Intestine	intestine
2	chr15:41101200-41110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:41101400-41109600	Strong transcription	Fetal Intestine Small	intestine
4	chr15:41101400-41115800	Weak transcription	A549	lung
5	chr15:41103400-41110400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:41103800-41115600	Weak transcription	HepG2	liver
7	chr15:41104200-41115800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:41104600-41115800	Weak transcription	HMEC	breast
9	chr15:41106000-41117600	Weak transcription	Hela-S3	cervix
10	chr15:41106600-41109800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:41107000-41109400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:41107200-41109400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:41107200-41109400	Weak transcription	Osteobl	bone
14	chr15:41107200-41110400	Weak transcription	Lung	lung
15	chr15:41107200-41135200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:41107400-41109600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:41107400-41109800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:41107400-41110000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:41107400-41110200	Weak transcription	Fetal Brain Female	brain
20	chr15:41107400-41110600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:41107400-41115400	Weak transcription	Fetal Intestine Large	intestine
22	chr15:41107400-41118000	Weak transcription	Gastric	stomach
23	chr15:41107600-41109400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:41107600-41109800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:41107600-41109800	Weak transcription	Stomach Mucosa	stomach
26	chr15:41107600-41110200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:41107600-41117600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:41107600-41117600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:41107600-41120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:41107600-41135200	Weak transcription	Esophagus	oesophagus
31	chr15:41107800-41109400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:41107800-41109400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:41107800-41109600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:41107800-41109600	Weak transcription	Right Atrium	heart
35	chr15:41107800-41109800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:41107800-41109800	Weak transcription	Adipose Nuclei	Adipose
37	chr15:41107800-41110000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:41107800-41110000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr15:41107800-41110200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:41107800-41110400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr15:41107800-41115800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr15:41107800-41116000	Weak transcription	NHEK	skin
43	chr15:41108000-41109600	Weak transcription	Primary B cells from cord blood	blood
44	chr15:41108000-41109600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:41108000-41109600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:41108000-41109800	Weak transcription	Primary T cells from cord blood	blood
47	chr15:41108000-41110200	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:41108000-41110200	Weak transcription	Fetal Thymus	thymus
49	chr15:41108000-41110800	Weak transcription	K562	blood
50	chr15:41108200-41111200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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