Variant report

Variant	rs9884239
Chromosome Location	chr4:151096638-151096639
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10001645	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10001651	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10020361	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10029811	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033999	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12019295	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17026748	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28361896	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28377256	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28501175	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28598870	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28616626	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635652	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28673979	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4353883	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59085186	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60526300	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338194	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62338212	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62338216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72732403	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7438777	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9884665	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997755	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]

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	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3412514	chr4:151095502-151097400	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9884239	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:151085400-151097400	Weak transcription	Ovary	ovary
3	chr4:151089200-151097000	Weak transcription	Aorta	Aorta
4	chr4:151091600-151104800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:151092000-151097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:151092200-151096800	Weak transcription	NHDF-Ad	bronchial
7	chr4:151093000-151096800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:151094200-151098200	Enhancers	Fetal Muscle Leg	muscle
9	chr4:151094800-151097400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:151095000-151097000	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:151095000-151097200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:151095000-151097200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:151095200-151096800	Weak transcription	Fetal Kidney	kidney
14	chr4:151095200-151097200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:151095200-151097400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:151095200-151097400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:151095400-151097000	Weak transcription	Pancreas	Pancrea
18	chr4:151095400-151097200	Weak transcription	HSMM	muscle
19	chr4:151095400-151097400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:151095400-151097400	Weak transcription	Right Atrium	heart
21	chr4:151095400-151098000	Enhancers	Brain Anterior Caudate	brain
22	chr4:151095400-151100000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:151095400-151101400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:151095600-151096800	Enhancers	Fetal Heart	heart
25	chr4:151095600-151097000	Weak transcription	Brain Angular Gyrus	brain
26	chr4:151095600-151097000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:151095600-151097000	Weak transcription	Fetal Brain Female	brain
28	chr4:151095600-151097200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:151095600-151097200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:151095600-151097200	Weak transcription	Fetal Lung	lung
31	chr4:151095600-151097200	Weak transcription	Osteobl	bone
32	chr4:151095600-151097400	Weak transcription	NH-A	brain
33	chr4:151095600-151097400	Weak transcription	NHLF	lung
34	chr4:151095600-151097600	Weak transcription	Brain Substantia Nigra	brain
35	chr4:151095600-151097600	Weak transcription	A549	lung
36	chr4:151095800-151097200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:151095800-151097200	Weak transcription	Adipose Nuclei	Adipose
38	chr4:151095800-151097400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:151095800-151097400	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:151096000-151096800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:151096000-151099800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:151096200-151100000	Enhancers	HSMMtube	muscle
43	chr4:151096400-151097200	Enhancers	Brain Germinal Matrix	brain
44	chr4:151096400-151097800	Enhancers	Stomach Smooth Muscle	stomach
45	chr4:151096400-151098000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr4:151096400-151098000	Enhancers	Left Ventricle	heart
47	chr4:151096400-151100000	Enhancers	Fetal Brain Male	brain
48	chr4:151096600-151096800	Enhancers	Fetal Muscle Trunk	muscle
49	chr4:151096600-151097600	Enhancers	Lung	lung
50	chr4:151096600-151097600	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links