Variant report

Variant	rs2412508
Chromosome Location	chr15:40593431-40593432
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	EP300	chr15:40593381-40594574	SK-N-SH	brain:	n/a	chr15:40593964-40593977
2	MXI1	chr15:40593375-40594268	SK-N-SH	brain:	n/a	n/a

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

Variant related genes	Relation type
PLCB2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1869901	0.98[LWK][hapmap];0.98[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs1869902	0.88[EUR][1000 genomes]
rs1869903	0.87[ASN][1000 genomes]
rs2305647	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	0.84[ASN][1000 genomes]
rs2898991	0.94[AFR][1000 genomes]
rs3765064	0.82[ASN][1000 genomes]
rs3784397	0.83[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[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	0.82[ASN][1000 genomes]
rs59341305	0.87[ASN][1000 genomes]
rs60309188	0.87[ASN][1000 genomes]
rs7162043	0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412508	INO80	cis	lymphoblastoid	seeQTL

Chromatin state (count:62 , 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	chr15:40589200-40593800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:40589400-40593800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:40590000-40599600	Weak transcription	Pancreas	Pancrea
19	chr15:40590800-40596000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:40591000-40597600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:40591400-40598200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:40591600-40598800	Weak transcription	Right Atrium	heart
23	chr15:40592800-40593800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr15:40592800-40594600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr15:40592800-40595200	Strong transcription	Dnd41	blood
26	chr15:40593000-40594600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:40593000-40594600	Enhancers	Left Ventricle	heart
28	chr15:40593000-40594800	Enhancers	Right Ventricle	heart
29	chr15:40593000-40595000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:40593000-40596600	Genic enhancers	Monocytes-CD14+_RO01746	blood
31	chr15:40593000-40596800	Strong transcription	Primary T cells from cord blood	blood
32	chr15:40593000-40596800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:40593000-40598200	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr15:40593200-40593600	Enhancers	Fetal Stomach	stomach
35	chr15:40593200-40593800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:40593200-40594000	Strong transcription	Fetal Thymus	thymus
37	chr15:40593200-40594000	Flanking Active TSS	K562	blood
38	chr15:40593200-40594200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr15:40593200-40594200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:40593200-40594600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr15:40593200-40594600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:40593200-40595200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr15:40593200-40595200	Enhancers	Placenta	Placenta
44	chr15:40593200-40595400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:40593200-40596200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:40593200-40596600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:40593200-40597000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:40593200-40597600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr15:40593200-40597600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:40593200-40598800	Weak transcription	Rectal Smooth Muscle	rectum

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