Variant report

Variant	rs62344697
Chromosome Location	chr4:151408045-151408046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11721723	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722416	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11724676	0.84[EUR][1000 genomes]
rs11726007	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11726346	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11727758	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11727995	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11728230	0.84[EUR][1000 genomes]
rs11728745	0.85[AFR][1000 genomes]
rs11729560	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11729564	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11731650	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11733079	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11734641	0.85[AFR][1000 genomes]
rs11734774	0.85[AFR][1000 genomes]
rs11736470	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11736546	0.84[EUR][1000 genomes]
rs11737261	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11737450	0.85[AFR][1000 genomes]
rs11930294	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11932482	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11933088	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11934033	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11936019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11936496	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11936646	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11937036	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11940101	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11946076	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1507190	0.85[AFR][1000 genomes]
rs17504373	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17504602	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17504868	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17588916	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17588965	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17589182	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17589398	0.80[ASN][1000 genomes]
rs2056457	0.85[AFR][1000 genomes]
rs2271043	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2292122	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35750119	0.85[AFR][1000 genomes]
rs36187100	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4370117	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4413388	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4419457	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4593110	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696084	0.85[AFR][1000 genomes]
rs4696134	0.84[EUR][1000 genomes]
rs4696185	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4696299	0.85[AFR][1000 genomes]
rs4696320	0.84[EUR][1000 genomes]
rs4696458	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55770979	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55875525	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55889963	0.85[AFR][1000 genomes]
rs55977492	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55998463	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56004102	0.85[AFR][1000 genomes]
rs56397289	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56398631	0.85[AFR][1000 genomes]
rs56401050	0.84[EUR][1000 genomes]
rs56671775	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57452017	0.81[ASN][1000 genomes]
rs58633621	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60557777	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61269060	0.85[AFR][1000 genomes]
rs62344660	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62344663	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62344664	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62344694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62344699	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62344702	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62344705	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62344742	0.81[ASN][1000 genomes]
rs62346990	0.85[AFR][1000 genomes]
rs62347033	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62347034	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62347035	0.84[EUR][1000 genomes]
rs62347038	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62347043	0.84[EUR][1000 genomes]
rs62347044	0.84[EUR][1000 genomes]
rs62348573	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62348574	0.84[EUR][1000 genomes]
rs62348579	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62348580	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62348581	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72734403	0.85[AFR][1000 genomes]
rs72734450	0.84[EUR][1000 genomes]
rs72734459	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72734461	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72734468	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72734475	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72734477	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72734478	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72734489	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72734495	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7690365	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs952098	0.83[AMR][1000 genomes];0.84[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
rs62344697	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151356600-151411200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr4:151364600-151414800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:151374400-151419000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:151376200-151409600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:151377000-151412400	Weak transcription	Liver	Liver
6	chr4:151380000-151409600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:151381200-151408200	Weak transcription	Left Ventricle	heart
8	chr4:151381400-151411400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:151382400-151422400	Weak transcription	Adipose Nuclei	Adipose
10	chr4:151384600-151409800	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:151385400-151442200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:151386000-151408800	Weak transcription	Pancreas	Pancrea
13	chr4:151387600-151408200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:151387600-151409800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:151387600-151412600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:151387600-151419000	Weak transcription	K562	blood
17	chr4:151387800-151423000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:151390600-151411400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:151391800-151411400	Weak transcription	Fetal Intestine Large	intestine
20	chr4:151392200-151413000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr4:151392200-151414800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:151392200-151424400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:151395200-151416800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:151395400-151424000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:151396200-151409600	Weak transcription	Dnd41	blood
26	chr4:151397400-151411000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:151398600-151411200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:151398600-151415000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:151399400-151411200	Weak transcription	GM12878-XiMat	blood
30	chr4:151399400-151411400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:151399600-151413000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr4:151400000-151434200	Weak transcription	Primary T cells from cord blood	blood
33	chr4:151400400-151422000	Weak transcription	Osteobl	bone
34	chr4:151406000-151408400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:151406200-151409000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:151406200-151416200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:151406400-151410000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:151407000-151411200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:151407000-151412600	Weak transcription	Fetal Kidney	kidney
40	chr4:151407200-151408400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr4:151407200-151411200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:151407800-151409000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:151408000-151408400	Strong transcription	Primary B cells from cord blood	blood
44	chr4:151408000-151408400	Strong transcription	Rectal Mucosa Donor 29	rectum

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