Variant report

Variant	rs28646031
Chromosome Location	chr4:151070434-151070435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151065674..151068783-chr4:151069402..151072348,3	MCF-7	breast:
2	chr4:151057757..151060556-chr4:151069534..151071946,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10001334	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723944	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735949	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737128	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435185	0.93[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420313	0.85[EUR][1000 genomes]
rs28530482	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28589304	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28632044	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28687892	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56849087	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60907583	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338191	0.95[AFR][1000 genomes];0.93[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[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662296	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662889	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662896	0.98[AFR][1000 genomes];0.97[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	0.86[AFR][1000 genomes];0.92[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
rs28646031	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr4:151057800-151070600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:151061800-151071800	Weak transcription	Brain Anterior Caudate	brain
5	chr4:151062800-151071800	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:151062800-151072000	Weak transcription	Aorta	Aorta
7	chr4:151063000-151070800	Weak transcription	HSMMtube	muscle
8	chr4:151063200-151070600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:151063400-151070600	Weak transcription	Fetal Heart	heart
10	chr4:151064600-151080200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:151066400-151071800	Weak transcription	Fetal Stomach	stomach
12	chr4:151067400-151071400	Weak transcription	NHLF	lung
13	chr4:151067400-151074200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:151067800-151070600	Weak transcription	A549	lung
15	chr4:151067800-151071800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:151067800-151074200	Weak transcription	HSMM	muscle
17	chr4:151068000-151070600	Weak transcription	Brain Germinal Matrix	brain
18	chr4:151068000-151074000	Weak transcription	Brain Substantia Nigra	brain
19	chr4:151069600-151075400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:151070000-151071400	Enhancers	Rectal Smooth Muscle	rectum
21	chr4:151070000-151071800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:151070000-151072600	Enhancers	Ovary	ovary
23	chr4:151070200-151070600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:151070200-151071800	Weak transcription	Left Ventricle	heart
25	chr4:151070400-151071200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:151070400-151071400	Enhancers	Osteobl	bone
27	chr4:151070400-151071600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:151070400-151071600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:151070400-151072200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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