Variant report

Variant	rs62346996
Chromosome Location	chr4:151280308-151280309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:151274057..151276592-chr4:151280241..151282352,2	K562	blood:
2	chr4:151269841..151272760-chr4:151278468..151280411,2	K562	blood:
3	chr4:151278776..151280327-chr4:151281874..151283378,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11723215	0.84[AMR][1000 genomes]
rs11724676	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11726007	0.83[AMR][1000 genomes]
rs11726346	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11728230	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11728745	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11729564	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11731650	0.83[AMR][1000 genomes]
rs11733079	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11734242	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11734641	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11734774	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11736470	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11736546	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11737450	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11930294	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11933088	0.91[AMR][1000 genomes]
rs11934033	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11936496	0.83[AMR][1000 genomes]
rs11936646	0.83[AMR][1000 genomes]
rs11940101	0.83[AMR][1000 genomes]
rs11946076	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11946787	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1507190	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1507191	0.82[ASN][1000 genomes]
rs17504117	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17504373	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17504602	0.83[AMR][1000 genomes]
rs17588629	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17588916	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17588965	0.83[AMR][1000 genomes]
rs2056457	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2271043	0.83[AMR][1000 genomes]
rs2292122	0.83[AMR][1000 genomes]
rs35750119	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4370117	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4696083	0.82[AMR][1000 genomes]
rs4696084	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4696134	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4696299	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696320	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55770979	0.91[AMR][1000 genomes]
rs55795432	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55875525	0.83[AMR][1000 genomes]
rs55889963	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56004102	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs56198556	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56374126	0.80[ASN][1000 genomes]
rs56397289	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56398631	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs56401050	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58138000	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59713336	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60105956	0.82[AMR][1000 genomes]
rs60459852	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60557777	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61269060	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62346985	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62346990	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62347033	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62347034	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62347035	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62347038	0.93[AMR][1000 genomes]
rs62347043	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62347044	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62348573	0.93[AMR][1000 genomes]
rs62348574	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62348579	0.83[AMR][1000 genomes]
rs62348580	0.83[AMR][1000 genomes]
rs62348581	0.83[AMR][1000 genomes]
rs6834124	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72734403	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72734450	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72734459	0.83[AMR][1000 genomes]
rs72734461	0.81[AMR][1000 genomes]
rs952098	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][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
rs62346996	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151243000-151312000	Weak transcription	Primary B cells from cord blood	blood
2	chr4:151244200-151300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:151247800-151285200	Weak transcription	GM12878-XiMat	blood
4	chr4:151262400-151311200	Weak transcription	Primary T cells from cord blood	blood
5	chr4:151264400-151280400	Weak transcription	Small Intestine	intestine
6	chr4:151268800-151293800	Weak transcription	Fetal Intestine Small	intestine
7	chr4:151269800-151300600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:151270400-151285200	Weak transcription	Aorta	Aorta
9	chr4:151272000-151293800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:151272000-151298600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:151272000-151371400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:151272400-151294000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:151275400-151287600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:151277800-151287000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:151278200-151280600	Enhancers	Colon Smooth Muscle	Colon
16	chr4:151278600-151285400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:151279200-151298000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:151279400-151280600	Enhancers	Fetal Lung	lung
19	chr4:151279400-151287800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:151280000-151280600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:151280000-151280600	Enhancers	Fetal Stomach	stomach
22	chr4:151280000-151280800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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