Variant report

Variant	rs11921256
Chromosome Location	chr3:143228009-143228010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11915855	1.00[YRI][hapmap]
rs11918424	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs16853882	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv523529	chr3:143215472-143229569	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv518873	chr3:143220697-143237419	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11921256	LHX2	trans	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:143212600-143247400	Weak transcription	Primary T cells from cord blood	blood
3	chr3:143221200-143228200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:143223000-143256200	Weak transcription	Esophagus	oesophagus
5	chr3:143224800-143228800	Enhancers	Dnd41	blood
6	chr3:143225600-143228200	Weak transcription	Fetal Lung	lung
7	chr3:143225600-143228800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:143226400-143228400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:143226400-143230000	Weak transcription	Pancreas	Pancrea
10	chr3:143227000-143228800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:143227000-143230000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:143227200-143228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:143227200-143244400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:143227400-143228400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:143227400-143228600	Enhancers	HSMMtube	muscle
16	chr3:143227400-143233200	Weak transcription	Fetal Kidney	kidney
17	chr3:143227600-143228600	Enhancers	HSMM	muscle
18	chr3:143227800-143228200	Enhancers	Brain Substantia Nigra	brain
19	chr3:143227800-143231000	Weak transcription	Osteobl	bone
20	chr3:143228000-143230800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:143228000-143231400	Weak transcription	NHDF-Ad	bronchial
22	chr3:143228000-143243600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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