Variant report

Variant	rs56257633
Chromosome Location	chr15:55614509-55614510
allele	A/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	chr15:55612965..55617278-chr15:55620080..55622469,6	K562	blood:
3	chr15:55613382..55615549-chr15:55714258..55716081,2	K562	blood:
4	chr15:55612195..55616185-chr15:55619905..55621792,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260916	Chromatin interaction
ENSG00000261652	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10851588	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11071174	0.81[ASN][1000 genomes]
rs11071176	0.81[ASN][1000 genomes]
rs11071180	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11071181	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11490399	0.90[ASN][1000 genomes]
rs11629613	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11630409	0.83[ASN][1000 genomes]
rs11632757	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634665	0.81[ASN][1000 genomes]
rs11635303	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11635532	0.97[ASN][1000 genomes]
rs11636687	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11638111	0.92[ASN][1000 genomes]
rs11638732	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11639418	0.81[ASN][1000 genomes]
rs11639453	0.96[ASN][1000 genomes]
rs11855382	0.84[ASN][1000 genomes]
rs11857303	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];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	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290343	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290344	0.95[ASN][1000 genomes]
rs2305424	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2414409	0.90[ASN][1000 genomes]
rs28540063	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28636865	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28657774	0.94[ASN][1000 genomes]
rs28668016	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28680176	0.90[ASN][1000 genomes]
rs28706887	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28748576	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34848296	0.92[ASN][1000 genomes]
rs3743203	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774760	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774764	0.90[ASN][1000 genomes]
rs4774766	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55661134	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55933611	0.99[ASN][1000 genomes]
rs55957229	0.81[ASN][1000 genomes]
rs56159619	0.81[ASN][1000 genomes]
rs58701687	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60338710	0.85[ASN][1000 genomes]
rs60375490	0.81[ASN][1000 genomes]
rs61387252	0.81[ASN][1000 genomes]
rs61573749	0.85[ASN][1000 genomes]
rs67230579	0.97[ASN][1000 genomes]
rs67603645	0.92[ASN][1000 genomes]
rs7162777	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174876	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7183157	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7183960	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs72742273	0.96[ASN][1000 genomes]
rs72742282	0.91[ASN][1000 genomes]
rs8024695	0.83[ASN][1000 genomes]
rs8034229	0.80[ASN][1000 genomes]
rs9920058	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9920522	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	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
8	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
9	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
10	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
rs56257633	PIGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55616200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:55611800-55622400	Weak transcription	Left Ventricle	heart
3	chr15:55611800-55622400	Weak transcription	Lung	lung
4	chr15:55611800-55623200	Weak transcription	Spleen	Spleen
5	chr15:55611800-55623400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:55611800-55629600	Weak transcription	Pancreas	Pancrea
7	chr15:55611800-55640000	Weak transcription	Gastric	stomach
8	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
9	chr15:55612000-55616200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:55612000-55616400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:55612000-55616400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:55612000-55616800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:55612000-55620000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:55612000-55622200	Weak transcription	Esophagus	oesophagus
15	chr15:55612000-55622200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:55612000-55622400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:55612000-55628400	Weak transcription	Fetal Brain Male	brain
18	chr15:55612000-55629800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:55612000-55630600	Weak transcription	Ovary	ovary
20	chr15:55612000-55635400	Weak transcription	Fetal Brain Female	brain
21	chr15:55612000-55636000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:55612000-55636000	Weak transcription	Brain Germinal Matrix	brain
23	chr15:55612000-55636400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
26	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
27	chr15:55612200-55615200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:55612200-55616400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:55612400-55614800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr15:55612400-55617800	Weak transcription	Fetal Intestine Small	intestine
31	chr15:55612400-55623000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:55612400-55623400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:55612400-55623400	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:55612400-55625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr15:55612400-55627600	Weak transcription	Placenta	Placenta
36	chr15:55612400-55628200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:55612400-55631000	Weak transcription	HSMMtube	muscle
38	chr15:55612400-55635600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:55612600-55614600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr15:55612600-55614600	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr15:55612600-55614600	Weak transcription	Stomach Mucosa	stomach
42	chr15:55612600-55614800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:55612600-55615400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:55612600-55616000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:55612600-55616200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr15:55612600-55616400	Weak transcription	A549	lung
47	chr15:55612600-55617400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:55612600-55617600	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:55612600-55619600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:55612600-55619800	Weak transcription	Rectal Mucosa Donor 31	rectum

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