Variant report

Variant	rs1716178
Chromosome Location	chr12:123704598-123704599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123702115..123705680-chr12:123713540..123715755,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1051434	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10846489	0.92[AFR][1000 genomes]
rs11057189	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11057219	0.92[AFR][1000 genomes]
rs1109559	0.92[AFR][1000 genomes]
rs11610710	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11613128	0.81[AFR][1000 genomes]
rs12229700	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1568428	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1611973	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1616484	0.80[AFR][1000 genomes]
rs1619283	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1626703	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1716184	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727286	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1727293	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727295	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727301	0.89[ASN][1000 genomes]
rs1727305	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727312	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727319	0.82[EUR][1000 genomes]
rs1790088	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790096	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790104	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790106	0.82[AMR][1000 genomes]
rs1790121	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1790122	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1790129	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1790134	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1879379	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2337630	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2337631	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2682427	0.89[ASN][1000 genomes]
rs2851443	0.83[EUR][1000 genomes]
rs34841857	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs36121382	0.82[ASN][1000 genomes]
rs3759111	0.80[ASN][1000 genomes]
rs4460848	0.80[EUR][1000 genomes]
rs4553407	0.92[AFR][1000 genomes]
rs4759407	0.80[ASN][1000 genomes]
rs7139321	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7312955	0.85[AFR][1000 genomes]
rs73231928	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs949143	0.82[AMR][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	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
2	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1716178	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1716178	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1716178	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1716178	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1716178	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1716178	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
2	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:123652800-123707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123654000-123707000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:123654200-123712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123654200-123715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:123655000-123707200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:123655000-123708000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:123655000-123712000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:123674000-123706000	Weak transcription	HMEC	breast
13	chr12:123674600-123713400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:123678800-123706600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:123680600-123716600	Weak transcription	Colonic Mucosa	Colon
16	chr12:123684000-123707800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:123684000-123709800	Strong transcription	Liver	Liver
18	chr12:123685000-123708400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:123685400-123711600	Strong transcription	Fetal Stomach	stomach
20	chr12:123685800-123704600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:123685800-123707200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:123686200-123707200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:123687200-123711600	Strong transcription	Fetal Intestine Small	intestine
24	chr12:123687800-123705800	Weak transcription	Small Intestine	intestine
25	chr12:123687800-123707000	Weak transcription	Right Ventricle	heart
26	chr12:123687800-123716600	Weak transcription	Gastric	stomach
27	chr12:123687800-123716600	Weak transcription	Pancreas	Pancrea
28	chr12:123687800-123717000	Weak transcription	Aorta	Aorta
29	chr12:123688000-123715200	Weak transcription	Fetal Heart	heart
30	chr12:123689600-123712200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:123690600-123710800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:123690800-123716000	Weak transcription	Psoas Muscle	Psoas
33	chr12:123694600-123716800	Weak transcription	Ovary	ovary
34	chr12:123694800-123705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:123696000-123704600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:123696000-123706400	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:123696000-123706800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:123696000-123706800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:123696200-123706600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:123696200-123707800	Strong transcription	Dnd41	blood
41	chr12:123696200-123708200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:123696200-123709600	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:123696200-123715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:123696400-123704800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:123696400-123706800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr12:123696400-123710400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr12:123696400-123710600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:123696400-123711600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:123698400-123707200	Strong transcription	Fetal Thymus	thymus
50	chr12:123698400-123716600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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