Variant report

Variant	rs3784399
Chromosome Location	chr15:40598294-40598295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40588970..40591882-chr15:40594218..40598541,3	K562	blood:
2	chr15:40597155..40599934-chr15:40605080..40607975,2	K562	blood:
3	chr15:40588970..40591870-chr15:40597041..40599915,2	K562	blood:
4	chr15:40596629..40600129-chr15:40604012..40607975,4	K562	blood:
5	chr15:40572270..40573835-chr15:40597340..40599224,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244705	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000259198	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1123487	1.00[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305646	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3743138	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55927878	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56135201	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56203022	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62021888	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8023550	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3784399	PLCB2	cis	lymphoblastoid	seeQTL
rs3784399	C15orf23	cis	parietal	SCAN
rs3784399	TMEM85	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40584200-40599200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:40584200-40614800	Weak transcription	Gastric	stomach
3	chr15:40584400-40599000	Weak transcription	Liver	Liver
4	chr15:40589000-40599200	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:40590000-40599600	Weak transcription	Pancreas	Pancrea
6	chr15:40591600-40598800	Weak transcription	Right Atrium	heart
7	chr15:40593200-40598800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:40593200-40599200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:40593600-40598400	Weak transcription	Adipose Nuclei	Adipose
10	chr15:40594200-40598400	Weak transcription	Esophagus	oesophagus
11	chr15:40594200-40601000	Weak transcription	Fetal Lung	lung
12	chr15:40594400-40598400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40594600-40598400	Weak transcription	Left Ventricle	heart
14	chr15:40594600-40598600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:40594600-40598600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:40594600-40599200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:40594800-40598600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:40595000-40599600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:40595200-40598400	Weak transcription	Colonic Mucosa	Colon
20	chr15:40595200-40599400	Weak transcription	K562	blood
21	chr15:40595400-40598800	Weak transcription	Right Ventricle	heart
22	chr15:40595600-40598400	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr15:40595600-40598800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:40595800-40599000	Weak transcription	Lung	lung
25	chr15:40596000-40598800	Weak transcription	Fetal Heart	heart
26	chr15:40596200-40598400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:40596200-40598600	Weak transcription	Fetal Stomach	stomach
28	chr15:40596200-40599000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:40596600-40598400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:40596600-40598400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr15:40597000-40598400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:40597000-40598400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr15:40597000-40598400	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:40597000-40598600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr15:40597400-40598400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:40597600-40598400	Enhancers	Primary hematopoietic stem cells	blood
37	chr15:40597600-40598400	Enhancers	Fetal Thymus	thymus
38	chr15:40597600-40598600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr15:40597600-40598600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:40597600-40598600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr15:40597600-40602000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:40597800-40598400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:40597800-40601600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:40598000-40598600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:40598000-40598600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:40598000-40598600	Enhancers	Placenta	Placenta
47	chr15:40598000-40598600	Enhancers	Dnd41	blood
48	chr15:40598000-40599000	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr15:40598000-40599800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr15:40598000-40601800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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