Variant report

Variant	rs62344663
Chromosome Location	chr4:151377572-151377573
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151374833..151377803-chr4:151382991..151384523,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11721723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722416	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724676	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11726007	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11726346	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11727758	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727995	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11728230	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11729560	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729564	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11731650	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11733079	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11736470	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11736546	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11737261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930294	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11932482	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11933088	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11934033	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11936019	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11936496	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11936646	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11937036	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11940101	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11946076	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17504373	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17504602	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17504868	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17588916	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17588965	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17589182	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271043	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2292122	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36187100	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4370117	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4413388	0.95[ASN][1000 genomes]
rs4419457	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4593110	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696134	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4696185	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4696320	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4696458	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55770979	0.85[EUR][1000 genomes]
rs55875525	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55977492	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55998463	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56397289	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56401050	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56671775	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58633621	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60557777	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62344660	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62344664	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344694	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344697	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62344699	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344702	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62344705	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62347033	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62347034	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62347035	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62347038	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62347043	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62347044	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62348573	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62348574	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62348579	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62348580	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62348581	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72734450	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72734459	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72734461	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72734468	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72734475	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72734477	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72734478	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72734489	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72734495	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7690365	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs952098	0.82[AMR][1000 genomes];0.85[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	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
4	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
5	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
6	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62344663	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151333000-151408000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:151344800-151387200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:151345000-151389000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:151356200-151386800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:151356600-151411200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:151356800-151391200	Weak transcription	Fetal Intestine Large	intestine
7	chr4:151358400-151398600	Weak transcription	GM12878-XiMat	blood
8	chr4:151364600-151387400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:151364600-151414800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:151372200-151402200	Weak transcription	Fetal Intestine Small	intestine
11	chr4:151373600-151398000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:151374400-151381200	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:151374400-151419000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:151375800-151383800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:151376000-151387800	Weak transcription	Brain Angular Gyrus	brain
16	chr4:151376200-151409600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:151376800-151377800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
18	chr4:151376800-151403800	Weak transcription	Ovary	ovary
19	chr4:151377000-151377800	ZNF genes & repeats	Primary B cells from cord blood	blood
20	chr4:151377000-151377800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:151377000-151378000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:151377000-151378000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:151377000-151378200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr4:151377000-151403400	Weak transcription	Aorta	Aorta
25	chr4:151377000-151412400	Weak transcription	Liver	Liver
26	chr4:151377200-151377600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
27	chr4:151377200-151378200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:151377200-151384000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:151377400-151377600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:151377400-151377600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:151377400-151377800	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:151377400-151378000	Strong transcription	Primary T cells from cord blood	blood

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