Variant report

Variant	rs62348580
Chromosome Location	chr4:151357598-151357599
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	chr4:151354749..151358319-chr4:151367984..151369817,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11721723	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11722416	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11724676	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11726007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726346	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11727758	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11727995	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11728230	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11729560	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11729564	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11731650	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11733079	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11736470	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11736546	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11737261	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11930294	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11932482	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11933088	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11934033	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11936019	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11936496	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11936646	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11937036	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11940101	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11946076	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11946787	0.83[AMR][1000 genomes]
rs17504373	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17504602	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17504868	0.80[EUR][1000 genomes]
rs17588916	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17588965	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17589182	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2271043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35750119	0.81[AMR][1000 genomes]
rs36187100	0.84[EUR][1000 genomes]
rs4370117	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4419457	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4593110	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4696134	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4696185	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4696299	0.83[AMR][1000 genomes]
rs4696320	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4696458	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55770979	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55795432	0.83[AMR][1000 genomes]
rs55875525	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55977492	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55998463	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56397289	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56401050	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56671775	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58633621	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60557777	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62344660	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62344663	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62344664	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62344694	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62344697	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62344699	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62344702	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62344705	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62346996	0.83[AMR][1000 genomes]
rs62347033	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62347034	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62347035	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62347038	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62347043	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62347044	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62348573	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62348574	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62348579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62348581	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72734450	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72734459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72734461	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72734468	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72734475	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72734477	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72734478	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72734489	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72734495	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7690365	0.83[EUR][1000 genomes]
rs952098	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	nsv869051	chr4:151347901-151737781	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62348580	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151272000-151371400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:151290200-151367400	Weak transcription	K562	blood
3	chr4:151292400-151361000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:151313200-151358200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr4:151313600-151358000	Weak transcription	GM12878-XiMat	blood
6	chr4:151315800-151359400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:151317400-151358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:151319000-151371000	Weak transcription	Left Ventricle	heart
9	chr4:151331400-151358800	Weak transcription	Liver	Liver
10	chr4:151333000-151357800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:151333000-151408000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:151337200-151363200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:151344800-151361600	Weak transcription	Gastric	stomach
14	chr4:151344800-151387200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:151345000-151357600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:151345000-151363000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:151345000-151366200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:151345000-151367000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:151345000-151389000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:151345200-151365800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:151345200-151371200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:151346600-151360600	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:151352600-151377000	Weak transcription	Primary B cells from cord blood	blood
24	chr4:151355200-151357600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:151355200-151360800	Weak transcription	Fetal Kidney	kidney
26	chr4:151355600-151357600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:151355600-151358000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:151355600-151359200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:151356200-151386800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:151356600-151357800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:151356600-151371800	Weak transcription	Fetal Intestine Small	intestine
32	chr4:151356600-151411200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:151356800-151358400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:151356800-151376800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr4:151356800-151377400	Weak transcription	Primary T cells from cord blood	blood
36	chr4:151356800-151391200	Weak transcription	Fetal Intestine Large	intestine

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