Variant report

Variant	rs13116727
Chromosome Location	chr4:151223437-151223438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11929842	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11933443	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11944163	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12505042	0.89[ASN][1000 genomes]
rs12643608	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12644110	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12711271	0.83[EUR][1000 genomes]
rs13121248	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1472842	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1599167	0.89[ASN][1000 genomes]
rs17504145	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1813134	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1870515	0.86[ASN][1000 genomes]
rs1960918	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290847	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2292206	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2292207	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35016840	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35370115	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35766906	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62344533	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6535728	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6837957	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6850249	0.89[ASN][1000 genomes]
rs6852979	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653994	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654538	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7655683	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7657477	0.89[ASN][1000 genomes]
rs7677474	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7677475	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7685302	0.89[ASN][1000 genomes]
rs962626	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv880257	chr4:151170387-151231371	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13116727	LRBA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
2	chr4:151192400-151232800	Weak transcription	Brain Substantia Nigra	brain
3	chr4:151202800-151223800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:151203800-151244400	Weak transcription	Fetal Thymus	thymus
5	chr4:151204000-151223800	Weak transcription	K562	blood
6	chr4:151204000-151244600	Weak transcription	Lung	lung
7	chr4:151204600-151236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:151204600-151242200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:151205000-151236400	Weak transcription	Primary B cells from cord blood	blood
10	chr4:151205000-151272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:151206800-151223800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:151206800-151223800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:151207200-151226600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:151207600-151241600	Weak transcription	Fetal Intestine Large	intestine
15	chr4:151208000-151230400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:151208600-151230400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:151210800-151231400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:151211200-151227000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:151211200-151236200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:151213400-151229000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:151213400-151242200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:151213600-151226600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:151213600-151231000	Weak transcription	Primary T cells from cord blood	blood
24	chr4:151213800-151236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:151221800-151231200	Weak transcription	Fetal Heart	heart
26	chr4:151221800-151236200	Weak transcription	Left Ventricle	heart
27	chr4:151221800-151259600	Weak transcription	Fetal Intestine Small	intestine
28	chr4:151222200-151229000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:151222800-151224200	Enhancers	Colon Smooth Muscle	Colon
30	chr4:151222800-151224600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:151222800-151224600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:151222800-151224600	Enhancers	Osteobl	bone
33	chr4:151222800-151224800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:151223000-151224200	Enhancers	NH-A	brain
35	chr4:151223000-151224400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:151223000-151224400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr4:151223000-151224400	Enhancers	HUVEC	blood vessel
38	chr4:151223200-151224200	Enhancers	Rectal Smooth Muscle	rectum
39	chr4:151223200-151224400	Enhancers	NHDF-Ad	bronchial
40	chr4:151223200-151224400	Enhancers	NHLF	lung
41	chr4:151223200-151226600	Weak transcription	A549	lung
42	chr4:151223200-151237600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:151223400-151224400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:151223400-151224400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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