Variant report

Variant	rs55889963
Chromosome Location	chr4:151252700-151252701
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	chr4:151251315..151253563-chr4:151269052..151271081,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10520053	0.81[AMR][1000 genomes]
rs1080195	0.83[AMR][1000 genomes]
rs11722135	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11723398	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11726346	0.83[AMR][1000 genomes]
rs11728745	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729564	0.83[AMR][1000 genomes]
rs11733079	0.83[AMR][1000 genomes]
rs11734242	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11734641	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734677	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736470	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11737203	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737450	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11930294	0.83[AMR][1000 genomes]
rs11933088	0.81[AMR][1000 genomes]
rs11934033	0.83[AMR][1000 genomes]
rs11936019	0.85[AFR][1000 genomes]
rs11946076	0.83[AMR][1000 genomes]
rs11946787	0.89[AMR][1000 genomes]
rs1507190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507191	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503902	0.81[AMR][1000 genomes]
rs17503964	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17504117	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17504373	0.83[AMR][1000 genomes]
rs17588629	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17588916	0.83[AMR][1000 genomes]
rs1824406	0.83[AMR][1000 genomes]
rs2056457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085722	0.82[AMR][1000 genomes]
rs35750119	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3749574	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4370117	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4696083	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696084	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696087	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696299	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[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	0.84[AMR][1000 genomes]
rs55795432	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55875525	0.85[AFR][1000 genomes]
rs56004102	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56169929	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs56198556	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56374126	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56397289	0.83[AMR][1000 genomes]
rs56398631	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58138000	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59713336	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60105956	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60459852	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60557777	0.83[AMR][1000 genomes]
rs61269060	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344508	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs62344542	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62344543	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62344544	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62344694	0.85[AFR][1000 genomes]
rs62344697	0.85[AFR][1000 genomes]
rs62346984	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62346985	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62346990	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62346996	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62347033	0.83[AMR][1000 genomes]
rs62347034	0.83[AMR][1000 genomes]
rs62347038	0.83[AMR][1000 genomes]
rs62348573	0.83[AMR][1000 genomes]
rs67227188	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6817154	0.81[AMR][1000 genomes]
rs6834124	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852279	0.83[AMR][1000 genomes]
rs72734403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656639	0.81[AMR][1000 genomes]
rs7657457	0.81[AMR][1000 genomes]
rs7686693	0.83[AMR][1000 genomes]
rs952098	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
rs55889963	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 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	chr4:151221800-151259600	Weak transcription	Fetal Intestine Small	intestine
3	chr4:151224000-151259000	Weak transcription	Ovary	ovary
4	chr4:151224200-151274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:151226800-151272400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:151227400-151269400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:151231600-151257800	Weak transcription	Liver	Liver
8	chr4:151232400-151255200	Weak transcription	Aorta	Aorta
9	chr4:151233400-151264200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:151233400-151264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:151233600-151253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:151236400-151272600	Weak transcription	Thymus	Thymus
13	chr4:151236600-151259000	Weak transcription	Left Ventricle	heart
14	chr4:151236800-151264200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:151238200-151270200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:151240600-151259000	Weak transcription	Pancreas	Pancrea
17	chr4:151242600-151268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:151242800-151273800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:151243000-151277000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:151243000-151277400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:151243000-151312000	Weak transcription	Primary B cells from cord blood	blood
22	chr4:151243800-151258600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:151244200-151300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:151245000-151270400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:151245200-151257800	Weak transcription	Fetal Stomach	stomach
26	chr4:151245400-151253400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:151245400-151253600	Weak transcription	Fetal Lung	lung
28	chr4:151245400-151253600	Weak transcription	Osteobl	bone
29	chr4:151245400-151257800	Weak transcription	NHLF	lung
30	chr4:151245400-151258600	Weak transcription	Spleen	Spleen
31	chr4:151245400-151259000	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:151245400-151264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:151245400-151268200	Weak transcription	Esophagus	oesophagus
34	chr4:151245600-151254400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:151245600-151258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:151245800-151268000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:151247000-151259000	Weak transcription	HSMMtube	muscle
38	chr4:151247200-151277000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:151247400-151264200	Weak transcription	Fetal Intestine Large	intestine
40	chr4:151247600-151269800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:151247800-151258000	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:151247800-151261600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:151247800-151261800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:151247800-151285200	Weak transcription	GM12878-XiMat	blood
45	chr4:151248000-151261800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:151248000-151268000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:151248200-151269800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:151248800-151261200	Weak transcription	Primary T cells from cord blood	blood
49	chr4:151249000-151254200	Weak transcription	Fetal Heart	heart
50	chr4:151249000-151261000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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