Variant report

Variant	rs58138000
Chromosome Location	chr4:151259663-151259664
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151257124..151260042-chr4:151261309..151264282,4	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10520053	0.81[AMR][1000 genomes]
rs1080195	0.83[AMR][1000 genomes]
rs11722135	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11723398	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11728745	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734242	0.81[AMR][1000 genomes]
rs11734641	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734677	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734774	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11737203	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11737450	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11946787	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1507190	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1507191	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17503902	0.81[AMR][1000 genomes]
rs17503964	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17504117	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17588629	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1824406	0.83[AMR][1000 genomes]
rs2056457	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2085722	0.82[AMR][1000 genomes]
rs35750119	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3749574	0.82[AMR][1000 genomes]
rs4696083	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696084	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696087	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696299	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4696646	0.83[AMR][1000 genomes]
rs4696651	0.83[AMR][1000 genomes]
rs4696659	0.83[AMR][1000 genomes]
rs4696660	0.83[AMR][1000 genomes]
rs55728314	0.83[AMR][1000 genomes]
rs55770979	0.81[AMR][1000 genomes]
rs55795432	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55889963	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56004102	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56169929	0.83[AMR][1000 genomes]
rs56198556	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56374126	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56398631	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59713336	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60105956	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60459852	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61269060	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62344508	0.84[AMR][1000 genomes]
rs62344542	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344543	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344544	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62346984	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62346985	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62346990	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62346996	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67227188	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6817154	0.81[AMR][1000 genomes]
rs6834124	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6852279	0.83[AMR][1000 genomes]
rs72734403	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7656639	0.81[AMR][1000 genomes]
rs7657457	0.81[AMR][1000 genomes]
rs7686693	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv880259	chr4:151210761-151367745	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv880260	chr4:151214038-151331191	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv830112	chr4:151243801-151431771	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58138000	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151205000-151272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:151224200-151274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:151226800-151272400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr4:151227400-151269400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:151233400-151264200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:151233400-151264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:151236400-151272600	Weak transcription	Thymus	Thymus
8	chr4:151236800-151264200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:151238200-151270200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:151242600-151268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:151242800-151273800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:151243000-151277000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:151243000-151277400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:151243000-151312000	Weak transcription	Primary B cells from cord blood	blood
15	chr4:151244200-151300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:151245000-151270400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:151245400-151264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:151245400-151268200	Weak transcription	Esophagus	oesophagus
19	chr4:151245800-151268000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:151247200-151277000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr4:151247400-151264200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:151247600-151269800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:151247800-151261600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:151247800-151261800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:151247800-151285200	Weak transcription	GM12878-XiMat	blood
26	chr4:151248000-151261800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:151248000-151268000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr4:151248200-151269800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:151248800-151261200	Weak transcription	Primary T cells from cord blood	blood
30	chr4:151249000-151261000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:151253600-151264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:151257800-151260000	Enhancers	Fetal Stomach	stomach
33	chr4:151257800-151260200	Enhancers	NHLF	lung
34	chr4:151258400-151260200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:151258600-151259800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr4:151258600-151259800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:151258800-151259800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:151258800-151259800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:151258800-151259800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:151258800-151259800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:151258800-151259800	Active TSS	Stomach Smooth Muscle	stomach
42	chr4:151258800-151259800	Enhancers	Osteobl	bone
43	chr4:151258800-151260000	Enhancers	Fetal Lung	lung
44	chr4:151259000-151259800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr4:151259000-151259800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:151259000-151259800	Enhancers	Fetal Muscle Leg	muscle
47	chr4:151259000-151259800	Enhancers	Ovary	ovary
48	chr4:151259000-151259800	Enhancers	HSMMtube	muscle
49	chr4:151259000-151259800	Enhancers	NHDF-Ad	bronchial
50	chr4:151259200-151259800	Enhancers	Colonic Mucosa	Colon

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