Variant report

Variant	rs28616626
Chromosome Location	chr4:151101787-151101788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10001645	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10001651	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10020361	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10029811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12019295	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17026748	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28361896	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28377256	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28501175	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28598870	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28635652	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28673979	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4353883	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59085186	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60526300	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338194	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62338212	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62338216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72732403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7438777	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9884239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884665	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997755	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28616626	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151091600-151104800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr4:151097400-151102800	Weak transcription	Fetal Thymus	thymus
3	chr4:151097600-151113800	Weak transcription	Aorta	Aorta
4	chr4:151097600-151129000	Weak transcription	Lung	lung
5	chr4:151098000-151102000	Weak transcription	Left Ventricle	heart
6	chr4:151098000-151102400	Weak transcription	Brain Angular Gyrus	brain
7	chr4:151098000-151102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:151098000-151102400	Weak transcription	Right Atrium	heart
9	chr4:151098000-151102800	Weak transcription	Ovary	ovary
10	chr4:151098200-151101800	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:151098200-151102400	Weak transcription	Adipose Nuclei	Adipose
12	chr4:151098200-151120000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:151098200-151128000	Weak transcription	Fetal Stomach	stomach
14	chr4:151098400-151102400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:151098400-151102400	Weak transcription	Brain Substantia Nigra	brain
16	chr4:151099200-151102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:151099800-151102000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:151100000-151101800	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:151100000-151102000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:151100000-151102400	Weak transcription	Fetal Brain Male	brain
21	chr4:151100000-151102600	Weak transcription	NH-A	brain
22	chr4:151100000-151102800	Weak transcription	HSMMtube	muscle
23	chr4:151100000-151107000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:151100000-151127800	Weak transcription	Osteobl	bone
25	chr4:151100200-151116800	Weak transcription	HSMM	muscle
26	chr4:151101000-151102400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:151101000-151104200	Enhancers	Fetal Brain Female	brain
28	chr4:151101200-151104200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:151101400-151102200	Enhancers	NHLF	lung
30	chr4:151101400-151103400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr4:151101400-151104200	Enhancers	Fetal Heart	heart
32	chr4:151101400-151104800	Enhancers	Brain Germinal Matrix	brain
33	chr4:151101600-151104400	Enhancers	Brain Anterior Caudate	brain
34	chr4:151101600-151127600	Weak transcription	Colon Smooth Muscle	Colon

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