Variant report

Variant	rs11574027
Chromosome Location	chr12:48287373-48287374
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48276795..48279456-chr12:48285534..48287746,2	MCF-7	breast:
2	chr12:48280571..48282115-chr12:48285370..48287447,2	K562	blood:
3	chr12:48282132..48284740-chr12:48286708..48289007,3	K562	blood:
4	chr12:48286982..48288519-chr12:48291804..48294615,2	K562	blood:

Extended variants
information (count: 6 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11168302	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11168305	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11574012	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581281	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58379944	1.00[EUR][1000 genomes];0.99[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	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11574027	PDGFD	trans	lymphoblastoid	seeQTL
rs11574027	LRRK2	trans	lymphoblastoid	seeQTL
rs11574027	ANXA5	trans	lymphoblastoid	seeQTL
rs11574027	RASSF6	trans	lymphoblastoid	seeQTL
rs11574027	ADCY6	cis	lymphoblastoid	seeQTL
rs11574027	FAM113B	cis	lymphoblastoid	seeQTL
rs11574027	FAM13A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48262000-48296800	Weak transcription	Aorta	Aorta
2	chr12:48277200-48289600	Weak transcription	Esophagus	oesophagus
3	chr12:48277200-48290600	Weak transcription	Gastric	stomach
4	chr12:48277200-48295000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:48277600-48287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:48277600-48289000	Weak transcription	Hela-S3	cervix
7	chr12:48278400-48287400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:48278400-48289600	Weak transcription	Stomach Mucosa	stomach
9	chr12:48278600-48287800	Strong transcription	NHEK	skin
10	chr12:48279200-48287400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:48281400-48287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:48281400-48287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:48283000-48287800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:48283200-48288400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:48283400-48287600	Weak transcription	Primary B cells from cord blood	blood
16	chr12:48283400-48287600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:48283400-48287600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:48283400-48289600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:48283400-48289800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:48283400-48293200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:48283600-48290000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:48283600-48290400	Weak transcription	Fetal Intestine Large	intestine
23	chr12:48284000-48289600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:48284600-48287400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:48284800-48287600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:48284800-48288200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:48285000-48294400	Weak transcription	Right Ventricle	heart
28	chr12:48285200-48290000	Strong transcription	Fetal Intestine Small	intestine
29	chr12:48285400-48287400	Weak transcription	GM12878-XiMat	blood
30	chr12:48285400-48289600	Weak transcription	Placenta	Placenta
31	chr12:48285800-48287400	Genic enhancers	Duodenum Mucosa	Duodenum
32	chr12:48285800-48287600	Genic enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:48286000-48287600	Enhancers	Lung	lung
34	chr12:48286000-48288200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:48286000-48288400	Genic enhancers	Osteobl	bone
36	chr12:48286000-48292800	Weak transcription	Small Intestine	intestine
37	chr12:48286200-48287600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:48286400-48287400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:48286400-48287400	Weak transcription	Spleen	Spleen
40	chr12:48286400-48287800	Weak transcription	Colonic Mucosa	Colon
41	chr12:48286400-48287800	Enhancers	NHDF-Ad	bronchial
42	chr12:48286600-48287600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:48286600-48287600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:48286600-48287800	Enhancers	NHLF	lung
45	chr12:48286600-48288000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:48286600-48288400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:48286600-48288400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:48286600-48288400	Enhancers	HSMM	muscle
49	chr12:48286800-48287800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:48286800-48290200	Weak transcription	Pancreas	Pancrea

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