Variant report

Variant	rs952098
Chromosome Location	chr4:151316677-151316678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:151315284..151318816-chr4:151320374..151325337,6	K562	blood:
2	chr4:151314752..151316835-chr4:151320252..151322487,2	K562	blood:
3	chr4:151315444..151317639-chr4:151319800..151322753,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11721723	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11723215	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11724676	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726007	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11726346	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11727758	0.84[EUR][1000 genomes]
rs11728230	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731650	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11733079	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11734242	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11734774	0.83[AMR][1000 genomes]
rs11736470	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736546	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11737261	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11930294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11933088	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11936019	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11936496	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11936646	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11940101	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11946076	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11946787	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1507190	0.83[AMR][1000 genomes]
rs17504117	0.83[AMR][1000 genomes]
rs17504373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17504602	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17588916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17588965	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2056457	0.83[AMR][1000 genomes]
rs2271043	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2292122	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35750119	0.91[AMR][1000 genomes]
rs4370117	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696134	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696299	0.93[AMR][1000 genomes]
rs4696320	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55770979	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55795432	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55875525	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55889963	0.83[AMR][1000 genomes]
rs56397289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56401050	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60557777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344660	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62344663	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62344694	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62344697	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62346990	0.84[AMR][1000 genomes]
rs62346996	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62347033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62347034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62347035	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62347038	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62347043	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62347044	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62348573	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62348574	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62348579	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62348580	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62348581	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6817572	0.80[EUR][1000 genomes]
rs72734403	0.83[AMR][1000 genomes]
rs72734450	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72734459	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72734461	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72734468	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72734475	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72734477	0.85[EUR][1000 genomes]
rs72734478	0.83[AMR][1000 genomes];0.84[EUR][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
rs952098	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 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	chr4:151286600-151355600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:151290200-151367400	Weak transcription	K562	blood
4	chr4:151292400-151361000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:151296000-151317200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:151307000-151348800	Weak transcription	Aorta	Aorta
7	chr4:151307200-151323400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:151307200-151324000	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:151307200-151324200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:151307200-151332400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:151309600-151332600	Weak transcription	Stomach Mucosa	stomach
12	chr4:151311600-151343800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:151312800-151332400	Weak transcription	Primary B cells from cord blood	blood
14	chr4:151313200-151358200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:151313600-151358000	Weak transcription	GM12878-XiMat	blood
16	chr4:151314000-151324200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:151314200-151324200	Weak transcription	Pancreas	Pancrea
18	chr4:151314600-151320600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:151314600-151320800	Weak transcription	Fetal Intestine Small	intestine
20	chr4:151314600-151332600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:151314600-151342800	Weak transcription	Primary T cells from cord blood	blood
22	chr4:151314800-151321000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:151315000-151320400	Weak transcription	Fetal Intestine Large	intestine
24	chr4:151315000-151324200	Weak transcription	Lung	lung
25	chr4:151315000-151324200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:151315000-151332600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:151315600-151344000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:151315800-151324200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:151315800-151325200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:151315800-151359400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:151316200-151318400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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