Variant report

Variant	rs28589304
Chromosome Location	chr4:151072685-151072686
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151066204..151068081-chr4:151071216..151073291,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10001334	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723944	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737128	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435185	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814207	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28366470	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420313	0.85[EUR][1000 genomes]
rs28530482	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28632044	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28646031	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687892	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56849087	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60907583	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338191	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535715	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6535716	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6826837	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662896	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670292	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7683407	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884660	0.84[EUR][1000 genomes];0.84[ASN][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
rs28589304	LRBA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:151049200-151074000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:151064600-151080200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:151067400-151074200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:151067800-151074200	Weak transcription	HSMM	muscle
6	chr4:151068000-151074000	Weak transcription	Brain Substantia Nigra	brain
7	chr4:151069600-151075400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:151070600-151072800	Enhancers	Brain Germinal Matrix	brain
9	chr4:151070800-151074200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:151070800-151080600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:151071000-151073600	Weak transcription	A549	lung
12	chr4:151071400-151091400	Weak transcription	Osteobl	bone
13	chr4:151071600-151072800	Enhancers	Fetal Heart	heart
14	chr4:151071600-151073600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:151071600-151080400	Weak transcription	NHLF	lung
16	chr4:151071600-151091600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:151071800-151073000	Enhancers	Left Ventricle	heart
18	chr4:151072000-151074200	Weak transcription	HSMMtube	muscle
19	chr4:151072200-151073800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:151072200-151074200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:151072200-151074200	Weak transcription	Right Atrium	heart
22	chr4:151072200-151074800	Weak transcription	Right Ventricle	heart
23	chr4:151072600-151072800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:151072600-151073600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:151072600-151073600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:151072600-151073800	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:151072600-151074000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:151072600-151074200	Weak transcription	Brain Anterior Caudate	brain
29	chr4:151072600-151074200	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:151072600-151074200	Weak transcription	Ovary	ovary
31	chr4:151072600-151074400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:151072600-151077200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:151072600-151088000	Weak transcription	Fetal Stomach	stomach
34	chr4:151072600-151089000	Weak transcription	Aorta	Aorta

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