Variant report

Variant	rs11112473
Chromosome Location	chr12:105729272-105729273
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	chr12:105727720..105729883-chr12:105739325..105740853,2	MCF-7	breast:
2	chr12:105628021..105630375-chr12:105728752..105731859,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10861400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861403	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861407	0.80[EUR][1000 genomes]
rs10861409	0.80[EUR][1000 genomes]
rs10861411	0.80[EUR][1000 genomes]
rs10861412	0.80[EUR][1000 genomes]
rs11112469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112475	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112482	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112483	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112484	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112485	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112486	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112487	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112488	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112492	0.80[EUR][1000 genomes]
rs11112493	0.80[EUR][1000 genomes]
rs12829692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831150	0.83[EUR][1000 genomes]
rs1432592	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888846	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34189496	0.85[EUR][1000 genomes]
rs34346262	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35325227	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35335704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35519603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6797	0.80[EUR][1000 genomes]
rs7131942	0.80[EUR][1000 genomes]
rs7302174	0.80[EUR][1000 genomes]
rs7954485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972183	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11112473	C12orf75	cis	Artery Tibial	GTEx
rs11112473	C12orf75	cis	Artery Aorta	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105725200-105734600	Weak transcription	Esophagus	oesophagus
2	chr12:105725600-105729800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr12:105725600-105730200	Weak transcription	Pancreas	Pancrea
4	chr12:105725600-105747200	Weak transcription	Gastric	stomach
5	chr12:105725800-105729800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:105725800-105734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:105726000-105730200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:105726000-105731200	Weak transcription	Hela-S3	cervix
9	chr12:105726000-105734600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:105726000-105734600	Weak transcription	Fetal Intestine Small	intestine
11	chr12:105726200-105729800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:105726200-105730000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr12:105726200-105731200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:105726200-105731200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:105726200-105731200	Weak transcription	HepG2	liver
16	chr12:105726200-105734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:105726800-105730200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:105727000-105729400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:105727000-105731000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:105727000-105734600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:105727200-105729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:105727200-105729400	Weak transcription	Stomach Mucosa	stomach
23	chr12:105727200-105729400	Weak transcription	Thymus	Thymus
24	chr12:105727200-105729800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr12:105727200-105730000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:105727200-105734400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:105727400-105729600	Weak transcription	Primary T cells from cord blood	blood
28	chr12:105727400-105729800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:105727400-105730000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr12:105727400-105734400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:105727600-105729400	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr12:105727800-105730600	Flanking Active TSS	GM12878-XiMat	blood
33	chr12:105727800-105737200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:105728000-105729600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:105728000-105729600	Weak transcription	Fetal Thymus	thymus
36	chr12:105728000-105729800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:105728000-105736000	Weak transcription	HUVEC	blood vessel
38	chr12:105728200-105729600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:105728200-105729800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:105728400-105729800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:105728400-105734600	Weak transcription	HSMMtube	muscle
42	chr12:105728600-105729400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:105728600-105729600	Enhancers	Dnd41	blood
44	chr12:105728600-105729800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:105728600-105729800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:105728600-105729800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:105728600-105729800	Weak transcription	Placenta	Placenta
48	chr12:105728600-105730000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:105728600-105734400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:105728600-105734600	Weak transcription	Fetal Stomach	stomach

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