Variant report

Variant	rs2456525
Chromosome Location	chr15:53080413-53080414
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	chr15:53079161..53080673-chr15:53143168..53145503,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM214A-1	chr15:53079958-53080605	NONHSAT043947

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10518694	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[EUR][1000 genomes]
rs2120450	0.87[EUR][1000 genomes]
rs2243790	0.89[CEU][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs2440315	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.95[ASN][1000 genomes]
rs2440316	0.97[ASN][1000 genomes]
rs2440322	0.91[EUR][1000 genomes]
rs2440376	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs2456506	0.98[ASN][1000 genomes]
rs2456507	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs2456522	0.96[EUR][1000 genomes]
rs2456523	0.85[ASN][1000 genomes]
rs2456524	0.96[EUR][1000 genomes]
rs2456526	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs2456529	0.89[EUR][1000 genomes]
rs2456530	0.89[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2456532	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs2460	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs28475375	0.85[EUR][1000 genomes]
rs60065065	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7180600	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv457142	chr15:53041887-53091896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv569427	chr15:53041887-53091896	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2456525	ORMDL3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53075400-53081000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
2	chr15:53075400-53082000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr15:53075600-53081200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:53075600-53082000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr15:53075600-53083600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr15:53075800-53082200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:53076400-53083800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr15:53076600-53080600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:53076600-53081800	Bivalent Enhancer	Spleen	Spleen
10	chr15:53077200-53080600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:53077400-53081600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:53077600-53080600	Bivalent Enhancer	Brain Hippocampus Middle	brain
13	chr15:53077800-53081200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr15:53077800-53081600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:53077800-53081800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:53078000-53081600	Bivalent Enhancer	Brain Germinal Matrix	brain
17	chr15:53078600-53081000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
18	chr15:53079000-53081600	Active TSS	Liver	Liver
19	chr15:53079200-53080600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:53079200-53081200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
21	chr15:53079200-53081800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr15:53079400-53081000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
23	chr15:53079600-53080600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:53079600-53081200	Bivalent/Poised TSS	HepG2	liver
25	chr15:53079800-53081400	Active TSS	Pancreas	Pancrea
26	chr15:53079800-53081800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:53080000-53080800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
28	chr15:53080000-53081200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
29	chr15:53080000-53081200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr15:53080000-53081600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
31	chr15:53080000-53081600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:53080000-53081600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
33	chr15:53080000-53081600	Bivalent Enhancer	Fetal Brain Female	brain
34	chr15:53080000-53081800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
35	chr15:53080000-53081800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:53080000-53082000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr15:53080000-53082400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:53080200-53080600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
39	chr15:53080200-53080600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
40	chr15:53080200-53080600	Bivalent Enhancer	Colon Smooth Muscle	Colon
41	chr15:53080200-53080800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr15:53080200-53081600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
43	chr15:53080200-53081600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:53080200-53081800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:53080200-53082000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:53080400-53080600	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:53080400-53080600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:53080400-53080600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr15:53080400-53080600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr15:53080400-53080600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle

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