Variant report

Variant	rs12050587
Chromosome Location	chr15:55627528-55627529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55626819..55629654-chr15:55698292..55701271,2	MCF-7	breast:
2	chr15:55621149..55623081-chr15:55626125..55628321,2	MCF-7	breast:
3	chr15:55609913..55611477-chr15:55626062..55628781,2	MCF-7	breast:
4	chr15:55626342..55628299-chr15:55638487..55640766,2	K562	blood:
5	chr15:55618646..55620160-chr15:55625270..55627647,2	K562	blood:

Variant related genes	Relation type
ENSG00000225973	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000261652	Chromatin interaction
ENSG00000069943	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10851588	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11071174	0.86[CHB][hapmap]
rs11071180	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11071181	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11490399	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11629613	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11632757	0.82[ASN][1000 genomes]
rs11635532	0.88[ASN][1000 genomes]
rs11636687	1.00[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs11638111	0.83[ASN][1000 genomes]
rs11638732	0.81[ASN][1000 genomes]
rs11639418	0.91[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap]
rs11639453	0.87[ASN][1000 genomes]
rs11855382	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857303	0.88[ASN][1000 genomes]
rs12050662	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050663	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050885	0.86[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs2290341	0.80[JPT][hapmap]
rs2290343	0.92[ASN][1000 genomes]
rs2290344	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2305424	0.85[ASN][1000 genomes]
rs2414409	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2444038	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28540063	0.87[ASN][1000 genomes]
rs28657774	0.93[ASN][1000 genomes]
rs28668016	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28680176	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28706887	0.94[ASN][1000 genomes]
rs28748576	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34848296	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743203	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4261468	0.81[CHD][hapmap]
rs4774760	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4774764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774766	0.82[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs55661134	0.90[ASN][1000 genomes]
rs55933611	0.90[ASN][1000 genomes]
rs56257633	0.90[ASN][1000 genomes]
rs58701687	0.87[ASN][1000 genomes]
rs60338710	0.81[ASN][1000 genomes]
rs61573749	0.81[ASN][1000 genomes]
rs67230579	0.87[ASN][1000 genomes]
rs67603645	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7162777	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7174876	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs7183157	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183960	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72742273	0.87[ASN][1000 genomes]
rs72742282	0.82[ASN][1000 genomes]
rs8024695	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9920058	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]
rs9920522	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];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12050587	RAB27A	cis	parietal	SCAN
rs12050587	PIGB	cis	Nerve Tibial	GTEx
rs12050587	PIGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55629600	Weak transcription	Pancreas	Pancrea
2	chr15:55611800-55640000	Weak transcription	Gastric	stomach
3	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
4	chr15:55612000-55628400	Weak transcription	Fetal Brain Male	brain
5	chr15:55612000-55629800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:55612000-55630600	Weak transcription	Ovary	ovary
7	chr15:55612000-55635400	Weak transcription	Fetal Brain Female	brain
8	chr15:55612000-55636000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:55612000-55636000	Weak transcription	Brain Germinal Matrix	brain
10	chr15:55612000-55636400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
13	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
14	chr15:55612400-55627600	Weak transcription	Placenta	Placenta
15	chr15:55612400-55628200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:55612400-55631000	Weak transcription	HSMMtube	muscle
17	chr15:55612400-55635600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:55612600-55629600	Weak transcription	HSMM	muscle
19	chr15:55612600-55629800	Weak transcription	Brain Substantia Nigra	brain
20	chr15:55612600-55630000	Weak transcription	Brain Angular Gyrus	brain
21	chr15:55612600-55640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
25	chr15:55612800-55629800	Weak transcription	Fetal Kidney	kidney
26	chr15:55612800-55631400	Weak transcription	NH-A	brain
27	chr15:55612800-55635800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:55612800-55640400	Weak transcription	NHLF	lung
29	chr15:55612800-55649600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:55613600-55631800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr15:55614800-55649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:55615200-55629400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:55615400-55629600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:55617000-55627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:55617000-55635400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:55617000-55635600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:55617200-55629400	Weak transcription	A549	lung
39	chr15:55617400-55631200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:55618800-55633800	Weak transcription	Stomach Mucosa	stomach
41	chr15:55619600-55630800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:55619600-55633600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:55619600-55633800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:55619600-55640000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:55619800-55632200	Strong transcription	Adipose Nuclei	Adipose
46	chr15:55619800-55635400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:55619800-55636000	Weak transcription	HMEC	breast
48	chr15:55619800-55637600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr15:55620800-55636800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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