Variant report

Variant	rs7662889
Chromosome Location	chr4:151074804-151074805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10001334	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723944	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735949	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737128	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435185	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814207	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28366470	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420313	0.83[EUR][1000 genomes]
rs28530482	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28589304	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28632044	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28646031	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687892	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56849087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60907583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338191	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535715	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6535716	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6826837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662296	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670292	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7683407	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884660	0.82[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
rs7662889	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 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	chr4:151064600-151080200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:151069600-151075400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:151070800-151080600	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:151071400-151091400	Weak transcription	Osteobl	bone
6	chr4:151071600-151080400	Weak transcription	NHLF	lung
7	chr4:151071600-151091600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:151072600-151077200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:151072600-151088000	Weak transcription	Fetal Stomach	stomach
10	chr4:151072600-151089000	Weak transcription	Aorta	Aorta
11	chr4:151073800-151075400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:151074000-151075000	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:151074000-151077200	Enhancers	Fetal Heart	heart
14	chr4:151074200-151075200	Enhancers	Left Ventricle	heart
15	chr4:151074200-151075200	Enhancers	Lung	lung
16	chr4:151074200-151075200	Enhancers	Ovary	ovary
17	chr4:151074200-151075400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr4:151074400-151081800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:151074400-151091800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:151074400-151094200	Weak transcription	NH-A	brain
21	chr4:151074600-151076600	Weak transcription	A549	lung
22	chr4:151074600-151079200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:151074600-151080400	Weak transcription	Brain Anterior Caudate	brain
24	chr4:151074600-151081400	Weak transcription	Brain Substantia Nigra	brain
25	chr4:151074600-151087800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:151074600-151090000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:151074600-151094000	Weak transcription	HSMMtube	muscle
28	chr4:151074600-151094600	Weak transcription	HSMM	muscle
29	chr4:151074800-151075200	Enhancers	Right Ventricle	heart
30	chr4:151074800-151081200	Weak transcription	Stomach Smooth Muscle	stomach

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