Variant report

Variant	rs515341
Chromosome Location	chr15:55649224-55649225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55648571..55650756-chr15:55651811..55654369,2	MCF-7	breast:
2	chr15:55648089..55651017-chr15:55698550..55701644,3	MCF-7	breast:
3	chr15:55635158..55636900-chr15:55648731..55651543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261652	Chromatin interaction
ENSG00000260916	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12902710	0.80[CHD][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap]
rs2439048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28459661	0.87[AFR][1000 genomes]
rs35715239	0.81[AFR][1000 genomes]
rs569333	0.85[AFR][1000 genomes]
rs574923	0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs678892	0.90[ASW][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8026689	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs8036345	1.00[ASW][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs8037056	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8040540	0.90[ASW][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv520799	chr15:55645661-55760522	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs515341	RAB27A	cis	cerebellum	SCAN
rs515341	PIGB	cis	Esophagus Muscularis	GTEx
rs515341	PIGB	cis	lung	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
4	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
5	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
8	chr15:55612800-55649600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:55623000-55652600	Weak transcription	Psoas Muscle	Psoas
12	chr15:55623800-55660200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:55626000-55649600	Weak transcription	HUVEC	blood vessel
14	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:55630400-55654600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:55630400-55675600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:55630600-55655800	Weak transcription	Brain Angular Gyrus	brain
18	chr15:55630600-55660200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:55630600-55663200	Weak transcription	Fetal Lung	lung
20	chr15:55630600-55667800	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:55630600-55668400	Weak transcription	Brain Substantia Nigra	brain
22	chr15:55630800-55652400	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:55630800-55683600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:55631000-55667800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:55631200-55663200	Weak transcription	Pancreas	Pancrea
26	chr15:55631200-55674000	Weak transcription	Placenta	Placenta
27	chr15:55631800-55649600	Weak transcription	NH-A	brain
28	chr15:55633600-55667200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:55635800-55675200	Weak transcription	Fetal Brain Male	brain
30	chr15:55636600-55657000	Weak transcription	Fetal Brain Female	brain
31	chr15:55636600-55678200	Weak transcription	Fetal Thymus	thymus
32	chr15:55636800-55649600	Weak transcription	HMEC	breast
33	chr15:55636800-55651000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:55636800-55652000	Weak transcription	Left Ventricle	heart
35	chr15:55636800-55666200	Weak transcription	Brain Germinal Matrix	brain
36	chr15:55637000-55660400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:55637000-55663000	Weak transcription	K562	blood
38	chr15:55637000-55663400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:55637000-55671400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:55637400-55680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:55638000-55658200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:55639600-55652600	Weak transcription	Ovary	ovary
44	chr15:55641000-55649400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:55641000-55651000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr15:55641000-55652600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:55641000-55654800	Weak transcription	HSMMtube	muscle
48	chr15:55641000-55655200	Weak transcription	Lung	lung
49	chr15:55641000-55667800	Weak transcription	Spleen	Spleen
50	chr15:55641000-55668000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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