Variant report

Variant	rs12884292
Chromosome Location	chr14:56738452-56738453
allele	C/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:4)

rs_ID	r²[population]
rs11624380	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs11626451	1.00[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs11628793	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12435921	1.00[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1044886	chr14:56689682-56834648	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv542104	chr14:56689682-56834648	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12884292	LGALS3	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56717800-56749600	Weak transcription	Fetal Thymus	thymus
2	chr14:56717800-56765400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:56718400-56755800	Weak transcription	Ovary	ovary
4	chr14:56718800-56751400	Weak transcription	Primary B cells from cord blood	blood
5	chr14:56724600-56755200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr14:56725400-56746800	Weak transcription	Dnd41	blood
7	chr14:56725600-56742200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:56729200-56740600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr14:56731200-56747800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:56731400-56748000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr14:56733200-56744000	Weak transcription	Gastric	stomach
12	chr14:56733800-56746400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr14:56734000-56750000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:56734800-56740800	Weak transcription	Esophagus	oesophagus
15	chr14:56735200-56755200	Weak transcription	Adipose Nuclei	Adipose
16	chr14:56735400-56741200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr14:56735800-56741800	Weak transcription	Fetal Intestine Small	intestine
18	chr14:56735800-56750200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr14:56735800-56751800	Weak transcription	Primary T cells from cord blood	blood
20	chr14:56735800-56765800	Weak transcription	NHLF	lung
21	chr14:56737400-56755800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:56737800-56738800	Enhancers	Aorta	Aorta
23	chr14:56737800-56738800	Enhancers	Lung	lung
24	chr14:56737800-56739200	Enhancers	Brain Cingulate Gyrus	brain
25	chr14:56737800-56739200	Enhancers	Pancreas	Pancrea
26	chr14:56737800-56739400	Strong transcription	Thymus	Thymus
27	chr14:56737800-56740200	Enhancers	NH-A	brain
28	chr14:56738000-56739200	Enhancers	Brain Germinal Matrix	brain
29	chr14:56738200-56738800	Enhancers	Brain Angular Gyrus	brain
30	chr14:56738200-56739200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr14:56738200-56741800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:56738200-56741800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr14:56738400-56738600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr14:56738400-56738600	Enhancers	Right Atrium	heart
35	chr14:56738400-56738600	Flanking Active TSS	HSMMtube	muscle
36	chr14:56738400-56738800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr14:56738400-56738800	Enhancers	Brain Substantia Nigra	brain
38	chr14:56738400-56738800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr14:56738400-56738800	Flanking Active TSS	HUVEC	blood vessel
40	chr14:56738400-56739000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr14:56738400-56739200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr14:56738400-56739200	Flanking Active TSS	Osteobl	bone
43	chr14:56738400-56739400	Enhancers	Left Ventricle	heart
44	chr14:56738400-56740000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr14:56738400-56740000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr14:56738400-56740000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr14:56738400-56740000	Enhancers	Brain Hippocampus Middle	brain
48	chr14:56738400-56740000	Enhancers	Right Ventricle	heart
49	chr14:56738400-56741400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:56738400-56741600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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