Variant report

Variant	rs55933611
Chromosome Location	chr15:55608051-55608052
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55607556..55615100-chr15:55699006..55703115,13	K562	blood:
2	chr15:55579295..55584870-chr15:55607881..55612970,10	K562	blood:
3	chr15:55607682..55613892-chr15:55697623..55703247,7	K562	blood:
4	chr15:55607488..55610247-chr15:55633602..55635929,2	K562	blood:

Variant related genes	Relation type
ENSG00000069974	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000261652	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10851588	0.91[ASN][1000 genomes]
rs11071174	0.81[ASN][1000 genomes]
rs11071176	0.81[ASN][1000 genomes]
rs11071180	0.95[ASN][1000 genomes]
rs11071181	0.91[ASN][1000 genomes]
rs11490399	0.90[ASN][1000 genomes]
rs11629613	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11630409	0.83[ASN][1000 genomes]
rs11632757	0.89[ASN][1000 genomes]
rs11634665	0.81[ASN][1000 genomes]
rs11635303	0.83[ASN][1000 genomes]
rs11635532	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636687	0.98[ASN][1000 genomes]
rs11638111	0.91[ASN][1000 genomes]
rs11638732	0.84[ASN][1000 genomes]
rs11639418	0.81[ASN][1000 genomes]
rs11639453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855382	0.83[ASN][1000 genomes]
rs11857303	0.97[ASN][1000 genomes]
rs12050587	0.90[ASN][1000 genomes]
rs12050662	0.90[ASN][1000 genomes]
rs12050663	0.90[ASN][1000 genomes]
rs12050885	0.81[ASN][1000 genomes]
rs12050905	0.86[ASN][1000 genomes]
rs2290341	0.80[AMR][1000 genomes]
rs2290343	0.93[ASN][1000 genomes]
rs2290344	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305424	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414409	0.89[ASN][1000 genomes]
rs28540063	0.96[ASN][1000 genomes]
rs28636865	0.81[ASN][1000 genomes]
rs28657774	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28668016	0.99[ASN][1000 genomes]
rs28680176	0.90[ASN][1000 genomes]
rs28706887	0.96[ASN][1000 genomes]
rs28748576	0.95[ASN][1000 genomes]
rs34848296	0.91[ASN][1000 genomes]
rs3743203	0.80[ASN][1000 genomes]
rs4774760	0.95[ASN][1000 genomes]
rs4774764	0.90[ASN][1000 genomes]
rs4774766	0.82[ASN][1000 genomes]
rs55661134	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55957229	0.81[ASN][1000 genomes]
rs56159619	0.81[ASN][1000 genomes]
rs56257633	0.99[ASN][1000 genomes]
rs58701687	0.96[ASN][1000 genomes]
rs60338710	0.84[ASN][1000 genomes]
rs60375490	0.81[ASN][1000 genomes]
rs61387252	0.81[ASN][1000 genomes]
rs61573749	0.84[ASN][1000 genomes]
rs67230579	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67603645	0.92[ASN][1000 genomes]
rs7162777	0.95[ASN][1000 genomes]
rs7174876	0.96[ASN][1000 genomes]
rs7183157	0.92[ASN][1000 genomes]
rs7183960	0.90[ASN][1000 genomes]
rs72742273	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72742282	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8024695	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9920058	0.92[ASN][1000 genomes]
rs9920522	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569522	chr15:55532211-55611126	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904241	chr15:55534342-55611126	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv904242	chr15:55550755-55611126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv569524	chr15:55558624-55612511	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55933611	PIGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55583200-55610400	Weak transcription	Pancreas	Pancrea
2	chr15:55597000-55610600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:55597400-55610600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:55597600-55610000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:55598000-55609800	Weak transcription	Fetal Brain Male	brain
6	chr15:55599000-55609000	Weak transcription	Brain Angular Gyrus	brain
7	chr15:55599000-55610800	Weak transcription	Aorta	Aorta
8	chr15:55601600-55609000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:55601800-55610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:55602000-55610600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:55602200-55609000	Weak transcription	Fetal Heart	heart
12	chr15:55602200-55609800	Weak transcription	HMEC	breast
13	chr15:55602600-55610600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:55602800-55610600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:55603400-55610200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:55603600-55609000	Weak transcription	NHDF-Ad	bronchial
17	chr15:55604400-55610600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:55604600-55610600	Weak transcription	Brain Germinal Matrix	brain
19	chr15:55605000-55610600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:55605000-55610800	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:55605200-55609600	Weak transcription	Gastric	stomach
22	chr15:55605200-55609800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:55605200-55610000	Weak transcription	A549	lung
24	chr15:55605200-55610400	Weak transcription	Right Ventricle	heart
25	chr15:55605200-55610600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:55605200-55610600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:55605200-55610600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:55605200-55610600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:55605200-55610600	Weak transcription	Fetal Brain Female	brain
30	chr15:55605200-55610600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:55605200-55610800	Weak transcription	Small Intestine	intestine
32	chr15:55605400-55609600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:55605400-55609600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:55605400-55609600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:55605400-55610600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:55605400-55610800	Weak transcription	NHLF	lung
37	chr15:55605600-55608200	Weak transcription	Dnd41	blood
38	chr15:55605600-55609000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:55605600-55609000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr15:55605600-55609000	Weak transcription	GM12878-XiMat	blood
41	chr15:55605600-55609000	Weak transcription	HepG2	liver
42	chr15:55605600-55609200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr15:55605600-55609400	Weak transcription	Primary B cells from cord blood	blood
44	chr15:55605600-55609600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:55605600-55609600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:55605600-55609600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:55605600-55609800	Weak transcription	Brain Anterior Caudate	brain
48	chr15:55605600-55609800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:55605600-55610000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:55605600-55610000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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