Variant report

Variant	rs56198556
Chromosome Location	chr4:151244467-151244468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:151233974..151236166-chr4:151243561..151246301,3	K562	blood:
2	chr4:151240646..151243046-chr4:151243526..151245377,2	K562	blood:
3	chr4:151236375..151241361-chr4:151242903..151246234,4	K562	blood:
4	chr4:151242129..151245111-chr4:151249733..151251799,3	K562	blood:
5	chr4:151233974..151240316-chr4:151243440..151247752,8	K562	blood:

Variant related genes	Relation type
ENSG00000198589	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11722135	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11723398	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11728745	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734641	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734677	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734774	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737203	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11946787	0.82[AMR][1000 genomes]
rs1507190	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507191	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503964	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17504117	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17588629	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2056457	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35750119	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4696083	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696084	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696087	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696299	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55795432	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55889963	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56004102	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56374126	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56398631	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58138000	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59713336	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60105956	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60459852	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61269060	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344508	0.81[AMR][1000 genomes]
rs62344542	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62344543	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62344544	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62346984	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62346985	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62346990	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62346996	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs67227188	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6834124	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72734403	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs56198556	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
2	chr4:151204000-151244600	Weak transcription	Lung	lung
3	chr4:151205000-151272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:151221800-151259600	Weak transcription	Fetal Intestine Small	intestine
5	chr4:151224000-151259000	Weak transcription	Ovary	ovary
6	chr4:151224200-151244800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:151224200-151274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:151224400-151244600	Weak transcription	NHLF	lung
9	chr4:151226000-151249000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:151226800-151272400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:151227400-151269400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:151227800-151248400	Weak transcription	Adipose Nuclei	Adipose
13	chr4:151230200-151244600	Weak transcription	Spleen	Spleen
14	chr4:151231600-151257800	Weak transcription	Liver	Liver
15	chr4:151232400-151255200	Weak transcription	Aorta	Aorta
16	chr4:151233000-151246600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:151233400-151244600	Weak transcription	Esophagus	oesophagus
18	chr4:151233400-151264200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:151233400-151264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:151233600-151253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:151234400-151244600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:151235200-151244600	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:151235200-151249600	Weak transcription	Gastric	stomach
24	chr4:151236400-151272600	Weak transcription	Thymus	Thymus
25	chr4:151236600-151251200	Weak transcription	Colonic Mucosa	Colon
26	chr4:151236600-151259000	Weak transcription	Left Ventricle	heart
27	chr4:151236800-151264200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:151238000-151245800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:151238200-151244800	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:151238200-151247800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr4:151238200-151270200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:151239000-151244600	Weak transcription	Fetal Stomach	stomach
33	chr4:151239000-151248600	Weak transcription	Right Ventricle	heart
34	chr4:151239800-151245200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:151240600-151259000	Weak transcription	Pancreas	Pancrea
36	chr4:151241000-151248600	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:151241200-151245000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:151241800-151245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:151242000-151244600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:151242200-151244800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:151242200-151246200	Weak transcription	Fetal Intestine Large	intestine
42	chr4:151242600-151246200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:151242600-151247000	Weak transcription	GM12878-XiMat	blood
44	chr4:151242600-151268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:151242800-151244600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:151242800-151246600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:151242800-151273800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:151243000-151244600	Weak transcription	K562	blood
49	chr4:151243000-151245000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:151243000-151246200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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