Variant report

Variant	rs4924508
Chromosome Location	chr15:41143340-41143341
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	chr15:41095336..41097635-chr15:41142803..41144806,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1049598	0.93[CEU][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17649	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3736287	1.00[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs3759797	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs58107694	0.95[ASN][1000 genomes]
rs582639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583031	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs643875	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs659232	0.93[CEU][hapmap]
rs661745	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662236	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs689594	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs689626	0.93[CEU][hapmap]
rs690435	0.92[ASN][1000 genomes]
rs690458	0.93[CEU][hapmap]
rs690467	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028552	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4924508	PLCB2	cis	uninvolved skin	skin_eQTL
rs4924508	RP11-111A22.1	cis	Artery Tibial	GTEx
rs4924508	SPINT1	cis	multi-tissue	Pritchard

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41152200	Weak transcription	Small Intestine	intestine
2	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
3	chr15:41140000-41144600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:41140000-41145200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:41140000-41149800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:41140000-41149800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:41140000-41150400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:41140200-41143600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:41140200-41144400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:41140200-41145200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:41140200-41145400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:41140200-41145600	Weak transcription	Primary B cells from cord blood	blood
13	chr15:41140200-41145800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:41140200-41148000	Weak transcription	Spleen	Spleen
15	chr15:41140200-41149600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr15:41140200-41149600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:41140200-41149800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:41140200-41150000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:41140400-41145400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:41140400-41149400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:41140400-41151200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:41140600-41145600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:41140600-41147800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:41140600-41149400	Strong transcription	NHEK	skin
25	chr15:41140600-41150000	Weak transcription	Fetal Kidney	kidney
26	chr15:41140600-41151600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:41140800-41145000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr15:41140800-41145800	Genic enhancers	Fetal Intestine Small	intestine
29	chr15:41140800-41146000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:41140800-41148600	Weak transcription	Stomach Mucosa	stomach
31	chr15:41140800-41149400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:41140800-41149600	Weak transcription	K562	blood
33	chr15:41141200-41152600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:41141400-41144000	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr15:41141400-41145600	Genic enhancers	Fetal Intestine Large	intestine
36	chr15:41141400-41146200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:41141400-41149000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:41141600-41149000	Strong transcription	HMEC	breast
39	chr15:41141800-41148800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr15:41141800-41149800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:41142000-41146200	Genic enhancers	Rectal Mucosa Donor 31	rectum
42	chr15:41142000-41149800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:41142400-41143800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:41142400-41149600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:41142600-41143400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr15:41142600-41144000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:41142600-41144400	Genic enhancers	Duodenum Mucosa	Duodenum
48	chr15:41142600-41145800	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr15:41142600-41148800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr15:41142600-41149400	Strong transcription	Lung	lung

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