Variant report

Variant	rs2412525
Chromosome Location	chr15:40867122-40867123
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40866258..40868658-chr15:40873477..40876647,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10152546	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1044474	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10518697	0.92[EUR][1000 genomes]
rs1058734	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070283	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630273	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633184	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637245	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637422	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324748	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12385982	0.92[EUR][1000 genomes]
rs12441754	0.84[EUR][1000 genomes]
rs12903817	0.88[EUR][1000 genomes]
rs12907442	0.80[EUR][1000 genomes]
rs12908316	0.89[EUR][1000 genomes]
rs12913296	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12913739	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915171	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12915636	0.93[EUR][1000 genomes]
rs13329076	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17673703	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17674454	0.92[EUR][1000 genomes]
rs17747423	0.92[EUR][1000 genomes]
rs17747633	0.92[EUR][1000 genomes]
rs1814541	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1814542	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28529389	0.80[EUR][1000 genomes]
rs28634695	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28647196	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28669075	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34739056	0.83[EUR][1000 genomes]
rs34824658	0.89[EUR][1000 genomes]
rs35127391	0.92[EUR][1000 genomes]
rs35684277	0.86[EUR][1000 genomes]
rs35842610	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923880	0.91[EUR][1000 genomes]
rs4924486	0.90[EUR][1000 genomes]
rs62019876	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62019879	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71471880	0.86[EUR][1000 genomes]
rs7165509	0.86[EUR][1000 genomes]
rs7170288	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175747	0.86[EUR][1000 genomes]
rs8029530	0.83[EUR][1000 genomes]
rs8036891	0.83[EUR][1000 genomes]
rs8037180	0.85[EUR][1000 genomes]
rs8038122	0.87[EUR][1000 genomes]
rs8042386	0.85[EUR][1000 genomes]
rs9920642	0.86[EUR][1000 genomes]
rs9920676	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	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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2412525	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs2412525	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2412525	RP11-111A22.1	cis	lung	GTEx
rs2412525	C15orf57	cis	Heart Left Ventricle	GTEx
rs2412525	C15orf57	cis	Artery Aorta	GTEx
rs2412525	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2412525	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs2412525	C15orf57	cis	Artery Tibial	GTEx
rs2412525	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs2412525	CCDC32	cis	multi-tissue	Pritchard
rs2412525	C15orf57	cis	Muscle Skeletal	GTEx
rs2412525	C15orf57	cis	lung	GTEx
rs2412525	C15orf57	cis	Nerve Tibial	GTEx
rs2412525	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs2412525	RAD51	cis	multi-tissue	Pritchard
rs2412525	C15orf57	cis	Stomach	GTEx
rs2412525	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2412525	C15orf57	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40862800-40875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:40863000-40868200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:40863000-40870200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:40863000-40875000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:40863000-40875000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:40863200-40867200	Strong transcription	Fetal Muscle Leg	muscle
7	chr15:40863200-40868600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:40863200-40868800	Weak transcription	Fetal Heart	heart
9	chr15:40863200-40869000	Weak transcription	Fetal Brain Male	brain
10	chr15:40863600-40867200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:40863600-40867200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:40863600-40867200	Strong transcription	Primary B cells from cord blood	blood
13	chr15:40863600-40867200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:40863600-40867200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:40863600-40867200	Strong transcription	Brain Anterior Caudate	brain
16	chr15:40863600-40867400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:40863600-40867400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:40863600-40867400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:40863600-40867400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:40863600-40867400	Strong transcription	Liver	Liver
21	chr15:40863600-40867400	Strong transcription	NHDF-Ad	bronchial
22	chr15:40863600-40867400	Strong transcription	NHEK	skin
23	chr15:40863600-40867600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:40863600-40867600	Strong transcription	Adipose Nuclei	Adipose
25	chr15:40863600-40867600	Strong transcription	Ovary	ovary
26	chr15:40863600-40867800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:40863600-40867800	Strong transcription	Brain Hippocampus Middle	brain
28	chr15:40863600-40868000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:40863600-40868000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:40863800-40867200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr15:40863800-40867200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:40863800-40867200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:40863800-40867200	Strong transcription	Fetal Thymus	thymus
34	chr15:40863800-40867400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:40863800-40867400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:40863800-40867400	Strong transcription	Primary T cells from cord blood	blood
37	chr15:40863800-40867400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:40863800-40867400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:40863800-40867400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:40863800-40867600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:40863800-40867600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:40863800-40867600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr15:40863800-40867600	Strong transcription	NHLF	lung
44	chr15:40863800-40867800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr15:40863800-40868000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:40863800-40868000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:40864000-40867200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:40864000-40867400	Strong transcription	Fetal Intestine Large	intestine
49	chr15:40864000-40867600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:40864000-40868000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links