Variant report

Variant	rs1639387
Chromosome Location	chr18:25758897-25758898
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	REST	chr18:25753848-25759305	H1-neurons	neurons:	n/a	chr18:25755466-25755484 chr18:25757352-25757365 chr18:25757917-25757930 chr18:25757156-25757166 chr18:25757884-25757897 chr18:25757531-25757544 chr18:25755471-25755480 chr18:25755465-25755485 chr18:25757535-25757544 chr18:25756837-25756850 chr18:25757251-25757259 chr18:25755425-25755438 chr18:25755469-25755482
2	TEAD4	chr18:25758674-25759153	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr18:25758148-25758995	HUVEC	blood vessel:	n/a	chr18:25758870-25758881 chr18:25758874-25758882 chr18:25758288-25758297
4	POLR2A	chr18:25758674-25759012	SK-N-SH	brain:	n/a	n/a
5	JUN	chr18:25758781-25759146	H1-hESC	embryonic stem cell:	n/a	chr18:25758870-25758881 chr18:25758874-25758882
6	MAZ	chr18:25755730-25758994	IMR90	lung:	n/a	chr18:25758449-25758459 chr18:25755757-25755767 chr18:25757917-25757926 chr18:25757262-25757272
7	EP300	chr18:25756704-25759078	SK-N-SH	brain:	n/a	chr18:25756843-25756859 chr18:25758726-25758740 chr18:25757926-25757942 chr18:25756834-25756850 chr18:25756837-25756853 chr18:25756740-25756756 chr18:25757716-25757725 chr18:25757893-25757902
8	SP1	chr18:25758657-25759068	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr18:25757863-25759125	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr18:25758750-25759017	ECC-1	luminal epithelium:	n/a	n/a
11	GATA3	chr18:25757833-25759158	SK-N-SH	brain:	n/a	n/a
12	JUND	chr18:25758161-25759024	H1-hESC	embryonic stem cell:	n/a	chr18:25758870-25758881 chr18:25758874-25758882 chr18:25758288-25758297
13	SP1	chr18:25758642-25759057	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr18:25758709-25759017	H1-neurons	neurons:	n/a	n/a
15	NRF1	chr18:25757157-25759200	SK-N-SH	brain:	n/a	chr18:25758449-25758458 chr18:25758014-25758023 chr18:25757264-25757273
16	POLR2A	chr18:25755267-25758935	IMR90	lung:	n/a	n/a
17	RAD21	chr18:25758062-25758910	H1-hESC	embryonic stem cell:	n/a	chr18:25758444-25758457 chr18:25758173-25758187 chr18:25758442-25758456 chr18:25758121-25758134

Variant related genes	Relation type
CDH2	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11564387	0.80[YRI][hapmap]
rs11564388	0.80[YRI][hapmap]
rs11564390	0.80[YRI][hapmap]
rs11564392	0.80[YRI][hapmap]
rs1231233	1.00[CEU][hapmap]
rs1231234	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes]
rs1231238	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1231239	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17446484	0.80[YRI][hapmap]
rs17446616	1.00[YRI][hapmap]
rs17446644	0.80[YRI][hapmap]
rs17469008	0.80[YRI][hapmap]
rs17494961	0.80[YRI][hapmap]
rs1789464	0.80[YRI][hapmap]
rs2628604	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8094132	0.80[YRI][hapmap]
rs961497	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946601	1.00[YRI][hapmap]
rs9950633	0.80[YRI][hapmap]
rs9956424	0.80[YRI][hapmap]
rs9958671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv9622	chr18:25749905-26032816	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3425660	chr18:25756154-25759202	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25749800-25759200	Active TSS	Right Ventricle	heart
2	chr18:25752400-25759600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:25752600-25759200	Active TSS	Right Atrium	heart
4	chr18:25753400-25759600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr18:25753600-25759200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr18:25754000-25759200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr18:25754200-25759000	Active TSS	Brain Angular Gyrus	brain
8	chr18:25754200-25759000	Active TSS	Brain Cingulate Gyrus	brain
9	chr18:25754200-25759600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr18:25754400-25759200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr18:25754400-25759200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr18:25754600-25759400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr18:25754800-25759000	Active TSS	Brain Anterior Caudate	brain
14	chr18:25755000-25759000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr18:25756000-25759000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:25756600-25759000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr18:25756600-25759000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr18:25756600-25759200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr18:25756600-25760800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:25756800-25759200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr18:25756800-25759600	Active TSS	Brain Germinal Matrix	brain
22	chr18:25756800-25759800	Active TSS	Fetal Brain Female	brain
23	chr18:25758200-25759000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr18:25758400-25759000	Flanking Active TSS	Dnd41	blood
25	chr18:25758400-25759200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr18:25758400-25759200	Active TSS	Fetal Heart	heart
27	chr18:25758600-25759000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr18:25758600-25759000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr18:25758600-25759000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr18:25758600-25759000	Flanking Active TSS	Osteobl	bone
31	chr18:25758600-25759200	Flanking Active TSS	A549	lung
32	chr18:25758600-25763800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:25758800-25759000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr18:25758800-25759000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:25758800-25759000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr18:25758800-25759000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr18:25758800-25759000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr18:25758800-25759000	Enhancers	Fetal Brain Male	brain
39	chr18:25758800-25759000	Enhancers	Fetal Kidney	kidney
40	chr18:25758800-25759000	Enhancers	HUVEC	blood vessel
41	chr18:25758800-25759000	Flanking Active TSS	NH-A	brain
42	chr18:25758800-25759200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr18:25758800-25759200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr18:25758800-25759600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr18:25758800-25759800	Enhancers	Brain Substantia Nigra	brain
46	chr18:25758800-25762400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr18:25758800-25763200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr18:25758800-25763600	Weak transcription	Liver	Liver
49	chr18:25758800-25763600	Weak transcription	HepG2	liver
50	chr18:25758800-25763600	Weak transcription	HSMMtube	muscle

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