Variant report

Variant	rs12273257
Chromosome Location	chr11:35288024-35288025
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	chr11:35282207..35284321-chr11:35287540..35289873,2	MCF-7	breast:
2	chr11:35287643..35289884-chr11:35306047..35307843,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11821102	0.88[JPT][hapmap]
rs12269851	1.00[GIH][hapmap]
rs12271153	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12290877	0.96[ASN][1000 genomes]
rs12292131	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2236274	0.96[ASN][1000 genomes]
rs3794092	0.94[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap]
rs7124363	1.00[GIH][hapmap]
rs7124645	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv832120	chr11:35277410-35490304	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12273257	TFEC	trans	lymphoblastoid	seeQTL
rs12273257	PLAG1	trans	lymphoblastoid	seeQTL
rs12273257	TXNDC3	trans	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35265800-35305800	Weak transcription	HepG2	liver
2	chr11:35270200-35292600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr11:35270400-35296400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:35270400-35307000	Weak transcription	Fetal Brain Male	brain
5	chr11:35282200-35297000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:35282200-35297000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:35282400-35289200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:35282400-35296600	Weak transcription	Aorta	Aorta
9	chr11:35282600-35288600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:35282600-35296800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:35283000-35289400	Weak transcription	NHDF-Ad	bronchial
12	chr11:35283000-35302000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:35283800-35288400	Weak transcription	NHLF	lung
14	chr11:35284600-35296600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:35284600-35300800	Weak transcription	Brain Angular Gyrus	brain
16	chr11:35284800-35296600	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:35285800-35289800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:35285800-35308800	Weak transcription	Gastric	stomach
19	chr11:35286000-35289600	Enhancers	Primary hematopoietic stem cells	blood
20	chr11:35286400-35293800	Weak transcription	Brain Anterior Caudate	brain
21	chr11:35287200-35288800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr11:35287200-35289600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr11:35287400-35288400	Weak transcription	Pancreas	Pancrea
24	chr11:35287400-35289800	Enhancers	HSMM	muscle
25	chr11:35287600-35288200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:35287600-35288200	Weak transcription	HSMMtube	muscle
27	chr11:35287600-35288600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:35287600-35289200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:35287600-35296200	Weak transcription	Liver	Liver
30	chr11:35287800-35288600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr11:35287800-35293000	Weak transcription	Fetal Brain Female	brain
32	chr11:35288000-35288400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr11:35288000-35288400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:35288000-35288800	Enhancers	Brain Germinal Matrix	brain
35	chr11:35288000-35290400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:35288000-35293000	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links