Variant report

Variant	rs11564411
Chromosome Location	chr18:25619301-25619302
allele	C/T
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	CEBPB	chr18:25619050-25619564	A549	lung:	n/a	chr18:25619298-25619306
2	NFYB	chr18:25619159-25619391	Hela-S3	cervix:	n/a	chr18:25619295-25619309 chr18:25619297-25619307 chr18:25619296-25619309 chr18:25619294-25619309 chr18:25619294-25619309
3	FOS	chr18:25619067-25619423	MCF10A-Er-Src	breast:	n/a	chr18:25619240-25619251 chr18:25619243-25619254 chr18:25619242-25619249 chr18:25619296-25619305 chr18:25619242-25619251 chr18:25619241-25619252
4	MYC	chr18:25619142-25619301	MCF10A-Er-Src	breast:	n/a	n/a
5	JUN	chr18:25619060-25619435	HUVEC	blood vessel:	n/a	chr18:25619243-25619254 chr18:25619242-25619249 chr18:25619296-25619305 chr18:25619242-25619251 chr18:25619241-25619252
6	NR3C1	chr18:25619031-25619343	A549	lung:	n/a	n/a
7	FOS	chr18:25619138-25619362	MCF10A-Er-Src	breast:	n/a	chr18:25619240-25619251 chr18:25619243-25619254 chr18:25619242-25619249 chr18:25619296-25619305 chr18:25619242-25619251 chr18:25619241-25619252
8	NR3C1	chr18:25619016-25619462	A549	lung:	n/a	n/a
9	NR3C1	chr18:25619038-25619429	A549	lung:	n/a	n/a
10	FOS	chr18:25619098-25619422	MCF10A-Er-Src	breast:	n/a	chr18:25619240-25619251 chr18:25619243-25619254 chr18:25619242-25619249 chr18:25619296-25619305 chr18:25619242-25619251 chr18:25619241-25619252
11	CREB1	chr18:25619145-25619343	A549	lung:	n/a	n/a
12	FOS	chr18:25619085-25619399	MCF10A-Er-Src	breast:	n/a	chr18:25619240-25619251 chr18:25619243-25619254 chr18:25619242-25619249 chr18:25619296-25619305 chr18:25619242-25619251 chr18:25619241-25619252
13	NR3C1	chr18:25619099-25619419	A549	lung:	n/a	n/a
14	NR3C1	chr18:25619010-25619392	A549	lung:	n/a	n/a
15	FOS	chr18:25619043-25619459	HUVEC	blood vessel:	n/a	chr18:25619240-25619251 chr18:25619243-25619254 chr18:25619242-25619249 chr18:25619296-25619305 chr18:25619242-25619251 chr18:25619241-25619252
16	NR3C1	chr18:25619098-25619393	A549	lung:	n/a	n/a
17	GATA2	chr18:25619140-25619539	HUVEC	blood vessel:	n/a	chr18:25619243-25619252
18	POLR2A	chr18:25618996-25619349	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CDH2	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11564286	1.00[AMR][1000 genomes]
rs11564309	1.00[AMR][1000 genomes]
rs11564318	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11564320	1.00[AMR][1000 genomes]
rs11564399	1.00[AMR][1000 genomes]
rs1228420	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17468310	0.83[YRI][hapmap]
rs17493084	1.00[AMR][1000 genomes]
rs17493423	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17493542	1.00[AMR][1000 genomes]
rs17493576	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17493744	1.00[EUR][1000 genomes]
rs17493926	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17494136	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17494276	1.00[AMR][1000 genomes]
rs17494388	1.00[AMR][1000 genomes]
rs17521540	1.00[AMR][1000 genomes]
rs17522229	1.00[CEU][hapmap]
rs17522236	0.88[EUR][1000 genomes]
rs17522285	1.00[CEU][hapmap]
rs17522436	0.82[EUR][1000 genomes]
rs17522464	1.00[AMR][1000 genomes]
rs1899644	1.00[AMR][1000 genomes]
rs1899645	1.00[AMR][1000 genomes]
rs488190	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs525524	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs635726	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7243533	1.00[AMR][1000 genomes]
rs8090262	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv833605	chr18:25467096-25643447	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25583800-25621400	Weak transcription	Right Ventricle	heart
2	chr18:25609800-25621600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr18:25615200-25624600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:25616800-25625000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr18:25617000-25619400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr18:25617000-25620000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr18:25617000-25620400	Weak transcription	Osteobl	bone
8	chr18:25617000-25625000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr18:25617000-25628800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr18:25617200-25619800	Weak transcription	Brain Hippocampus Middle	brain
11	chr18:25617200-25621200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr18:25617400-25619800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr18:25617400-25620200	Weak transcription	Brain Angular Gyrus	brain
14	chr18:25617400-25625000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr18:25617400-25625200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr18:25617600-25619800	Weak transcription	Brain Substantia Nigra	brain
17	chr18:25617800-25619600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr18:25617800-25621400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr18:25618000-25619600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr18:25618000-25624200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr18:25618000-25624200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr18:25618200-25620000	Weak transcription	Fetal Brain Female	brain
23	chr18:25618200-25620400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:25618200-25620600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr18:25618400-25631600	Weak transcription	Fetal Brain Male	brain
26	chr18:25618600-25620400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr18:25618800-25619800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr18:25618800-25620200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr18:25618800-25620600	Enhancers	HUVEC	blood vessel
30	chr18:25618800-25622000	Enhancers	Fetal Heart	heart
31	chr18:25619000-25619400	Enhancers	H9 Cell Line	embryonic stem cell
32	chr18:25619000-25619400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr18:25619000-25619400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr18:25619000-25619600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:25619000-25619600	Enhancers	HSMM	muscle
36	chr18:25619000-25619600	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr18:25619000-25620400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr18:25619000-25620400	Enhancers	Liver	Liver
39	chr18:25619000-25621200	Enhancers	A549	lung
40	chr18:25619000-25621600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr18:25619000-25621800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr18:25619000-25621800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr18:25619000-25621800	Enhancers	Brain Germinal Matrix	brain
44	chr18:25619000-25622400	Enhancers	NH-A	brain
45	chr18:25619200-25619400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr18:25619200-25619400	Enhancers	Left Ventricle	heart
47	chr18:25619200-25619600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr18:25619200-25619600	Weak transcription	Brain Anterior Caudate	brain
49	chr18:25619200-25619600	Enhancers	Right Atrium	heart
50	chr18:25619200-25620800	Enhancers	Fetal Lung	lung

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