Variant report

Variant	rs2305647
Chromosome Location	chr15:40593939-40593940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr15:40593699-40594081	K562	blood:	n/a	n/a
2	GTF2F1	chr15:40593852-40594032	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA2	chr15:40593594-40594071	SH-SY5Y	brain:	n/a	chr15:40593791-40593800 chr15:40593792-40593809 chr15:40593791-40593798
4	CBX3	chr15:40593623-40593940	K562	blood:	n/a	n/a
5	MYC	chr15:40593683-40593940	K562	blood:	n/a	n/a
6	CREB1	chr15:40593792-40594309	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr15:40593592-40593998	K562	blood:	n/a	n/a
8	TEAD4	chr15:40593533-40593983	K562	blood:	n/a	n/a
9	REST	chr15:40593637-40593988	K562	blood:	n/a	n/a
10	ZBTB7A	chr15:40593675-40594169	K562	blood:	n/a	chr15:40593910-40593919
11	MYC	chr15:40593629-40593945	K562	blood:	n/a	n/a
12	MAX	chr15:40593597-40593982	K562	blood:	n/a	n/a
13	UBTF	chr15:40593640-40593990	K562	blood:	n/a	n/a
14	ZNF143	chr15:40593888-40594034	H1-hESC	embryonic stem cell:	n/a	chr15:40593969-40593987 chr15:40593908-40593918
15	MAZ	chr15:40593677-40594057	K562	blood:	n/a	n/a
16	EP300	chr15:40593381-40594574	SK-N-SH	brain:	n/a	chr15:40593964-40593977
17	MXI1	chr15:40593375-40594268	SK-N-SH	brain:	n/a	n/a
18	SPI1	chr15:40593490-40593991	HL-60	blood:	n/a	n/a
19	JUND	chr15:40593664-40594186	K562	blood:	n/a	chr15:40594058-40594067
20	REST	chr15:40593620-40594080	SK-N-SH	brain:	n/a	chr15:40594015-40594025
21	TAL1	chr15:40593618-40593990	K562	blood:	n/a	chr15:40593791-40593809
22	TEAD4	chr15:40593908-40594250	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr15:40593614-40593972	H1-neurons	neurons:	n/a	n/a
24	TBL1XR1	chr15:40593743-40593940	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40592964..40595211-chr15:40658424..40661037,2	MCF-7	breast:
2	chr15:40593194..40594991-chr15:40625827..40627495,2	K562	blood:
3	chr15:40586469..40589558-chr15:40593473..40595451,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAK6-1	chr15:40593810-40594021	ENSG00000259307.1

Variant related genes	Relation type
PLCB2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1869901	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs1869902	0.88[EUR][1000 genomes]
rs1869903	0.91[ASN][1000 genomes]
rs2412508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28395841	0.88[ASN][1000 genomes]
rs2898991	0.94[AFR][1000 genomes]
rs3765064	0.86[ASN][1000 genomes]
rs3784397	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs3784398	0.94[AFR][1000 genomes]
rs41277676	0.88[EUR][1000 genomes]
rs55713690	0.91[EUR][1000 genomes]
rs57253140	0.86[ASN][1000 genomes]
rs59341305	0.91[ASN][1000 genomes]
rs60309188	0.91[ASN][1000 genomes]
rs7162043	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs72731484	0.88[EUR][1000 genomes]
rs72731485	0.91[EUR][1000 genomes]
rs72731486	0.88[EUR][1000 genomes]
rs72731496	0.88[EUR][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	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv904096	chr15:40550149-40604777	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv904097	chr15:40555065-40595627	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv517541	chr15:40557268-40595627	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv457118	chr15:40565705-40606484	Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv569227	chr15:40565705-40606484	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40578000-40596000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:40579000-40595200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:40579000-40595600	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr15:40579200-40597000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:40583800-40596400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:40584000-40594400	Weak transcription	Colonic Mucosa	Colon
7	chr15:40584000-40596400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:40584000-40596800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:40584200-40599200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:40584200-40614800	Weak transcription	Gastric	stomach
11	chr15:40584400-40599000	Weak transcription	Liver	Liver
12	chr15:40586800-40595600	Weak transcription	Brain Substantia Nigra	brain
13	chr15:40587200-40594200	Weak transcription	Fetal Brain Male	brain
14	chr15:40588000-40596000	Enhancers	Fetal Heart	heart
15	chr15:40589000-40599200	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:40590000-40599600	Weak transcription	Pancreas	Pancrea
17	chr15:40590800-40596000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:40591000-40597600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:40591400-40598200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:40591600-40598800	Weak transcription	Right Atrium	heart
21	chr15:40592800-40594600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
22	chr15:40592800-40595200	Strong transcription	Dnd41	blood
23	chr15:40593000-40594600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:40593000-40594600	Enhancers	Left Ventricle	heart
25	chr15:40593000-40594800	Enhancers	Right Ventricle	heart
26	chr15:40593000-40595000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:40593000-40596600	Genic enhancers	Monocytes-CD14+_RO01746	blood
28	chr15:40593000-40596800	Strong transcription	Primary T cells from cord blood	blood
29	chr15:40593000-40596800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:40593000-40598200	Genic enhancers	Primary monocytes fromperipheralblood	blood
31	chr15:40593200-40594000	Strong transcription	Fetal Thymus	thymus
32	chr15:40593200-40594000	Flanking Active TSS	K562	blood
33	chr15:40593200-40594200	Enhancers	H9 Cell Line	embryonic stem cell
34	chr15:40593200-40594200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:40593200-40594600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr15:40593200-40594600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:40593200-40595200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:40593200-40595200	Enhancers	Placenta	Placenta
39	chr15:40593200-40595400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:40593200-40596200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:40593200-40596600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:40593200-40597000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:40593200-40597600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr15:40593200-40597600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:40593200-40598800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:40593200-40599200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:40593400-40594200	Enhancers	Fetal Lung	lung
48	chr15:40593400-40594200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr15:40593400-40594400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:40593400-40594400	Weak transcription	Lung	lung

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