Variant report

Variant	rs9920058
Chromosome Location	chr15:55623377-55623378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55622982..55625062-chr15:55652852..55654704,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10851588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071174	0.91[CHB][hapmap]
rs11071180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11071181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11490399	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629613	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs11630409	0.80[ASN][1000 genomes]
rs11632757	0.82[ASN][1000 genomes]
rs11635303	0.81[ASN][1000 genomes]
rs11635532	0.88[ASN][1000 genomes]
rs11636687	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11638111	0.83[ASN][1000 genomes]
rs11638732	0.81[ASN][1000 genomes]
rs11639418	0.95[CHB][hapmap]
rs11639453	0.87[ASN][1000 genomes]
rs11855382	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857303	0.88[ASN][1000 genomes]
rs12050587	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050662	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050663	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050885	0.91[CHB][hapmap]
rs2290341	0.83[CHB][hapmap]
rs2290343	0.93[ASN][1000 genomes]
rs2290344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2305424	0.86[ASN][1000 genomes]
rs2414409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2444038	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28540063	0.88[ASN][1000 genomes]
rs28657774	0.95[ASN][1000 genomes]
rs28668016	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs28680176	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28706887	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28748576	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34848296	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743203	0.86[CHB][hapmap]
rs4774760	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4774764	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774766	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs55661134	0.91[ASN][1000 genomes]
rs55933611	0.92[ASN][1000 genomes]
rs56257633	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs58701687	0.88[ASN][1000 genomes]
rs60338710	0.81[ASN][1000 genomes]
rs61573749	0.81[ASN][1000 genomes]
rs67230579	0.89[ASN][1000 genomes]
rs67603645	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7162777	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7174876	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs7183157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72742273	0.87[ASN][1000 genomes]
rs72742282	0.83[ASN][1000 genomes]
rs8024695	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9920522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9920058	PIGB	Cis_1M	lymphoblastoid	RTeQTL
rs9920058	PIGB	cis	Nerve Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55623400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:55611800-55629600	Weak transcription	Pancreas	Pancrea
3	chr15:55611800-55640000	Weak transcription	Gastric	stomach
4	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
5	chr15:55612000-55628400	Weak transcription	Fetal Brain Male	brain
6	chr15:55612000-55629800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:55612000-55630600	Weak transcription	Ovary	ovary
8	chr15:55612000-55635400	Weak transcription	Fetal Brain Female	brain
9	chr15:55612000-55636000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:55612000-55636000	Weak transcription	Brain Germinal Matrix	brain
11	chr15:55612000-55636400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
14	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
15	chr15:55612400-55623400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:55612400-55623400	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:55612400-55625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:55612400-55627600	Weak transcription	Placenta	Placenta
19	chr15:55612400-55628200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:55612400-55631000	Weak transcription	HSMMtube	muscle
21	chr15:55612400-55635600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:55612600-55627200	Weak transcription	Fetal Lung	lung
23	chr15:55612600-55629600	Weak transcription	HSMM	muscle
24	chr15:55612600-55629800	Weak transcription	Brain Substantia Nigra	brain
25	chr15:55612600-55630000	Weak transcription	Brain Angular Gyrus	brain
26	chr15:55612600-55640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
30	chr15:55612800-55623400	Weak transcription	Osteobl	bone
31	chr15:55612800-55629800	Weak transcription	Fetal Kidney	kidney
32	chr15:55612800-55631400	Weak transcription	NH-A	brain
33	chr15:55612800-55635800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:55612800-55640400	Weak transcription	NHLF	lung
35	chr15:55612800-55649600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:55613600-55631800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:55614800-55649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:55615200-55629400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:55615400-55626600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:55615400-55629600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:55616600-55627200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr15:55617000-55627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:55617000-55635400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:55617000-55635600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:55617200-55629400	Weak transcription	A549	lung
47	chr15:55617400-55631200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:55618000-55626000	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:55618400-55623400	Weak transcription	Fetal Intestine Small	intestine
50	chr15:55618400-55624400	Strong transcription	Primary T cells fromperipheralblood	blood

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