Variant report

Variant	rs17468415
Chromosome Location	chr18:25625979-25625980
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	JUND	chr18:25625566-25626046	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr18:25625909-25626187	IMR90	lung:	n/a	chr18:25626054-25626064
3	BACH1	chr18:25625915-25626189	H1-hESC	embryonic stem cell:	n/a	n/a
4	YY1	chr18:25625866-25626203	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr18:25625889-25626199	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
CDH2	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11083244	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083247	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564295	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs11564298	0.89[YRI][hapmap]
rs11564398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564401	0.95[CEU][hapmap]
rs11564403	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564410	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564414	0.86[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11564418	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs11664205	0.87[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11664343	0.86[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1220027	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12454980	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956425	0.82[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12957702	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957780	0.87[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12971156	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1550662	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468213	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17468261	0.87[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17468443	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468699	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25617000-25628800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr18:25618400-25631600	Weak transcription	Fetal Brain Male	brain
3	chr18:25620400-25627400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:25620400-25627600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr18:25620400-25629200	Weak transcription	Left Ventricle	heart
6	chr18:25621600-25628200	Weak transcription	Fetal Brain Female	brain
7	chr18:25621800-25628200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr18:25623600-25627600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr18:25623600-25627600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:25624400-25627400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr18:25624600-25626000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr18:25624800-25626200	Enhancers	Brain Anterior Caudate	brain
13	chr18:25624800-25627400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr18:25624800-25627400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr18:25625000-25626000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr18:25625000-25626000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr18:25625000-25626200	Enhancers	Fetal Heart	heart
18	chr18:25625000-25626600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr18:25625000-25627400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr18:25625200-25626000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr18:25625200-25626000	Enhancers	Brain Cingulate Gyrus	brain
22	chr18:25625200-25626200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr18:25625200-25626200	Enhancers	Brain Angular Gyrus	brain
24	chr18:25625200-25626200	Enhancers	Brain Germinal Matrix	brain
25	chr18:25625200-25626200	Enhancers	A549	lung
26	chr18:25625200-25626200	Enhancers	Osteobl	bone
27	chr18:25625400-25626000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr18:25625400-25626000	Enhancers	HUVEC	blood vessel
29	chr18:25625400-25626200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:25625400-25626200	Enhancers	Brain Substantia Nigra	brain
31	chr18:25625400-25626200	Enhancers	HSMM	muscle
32	chr18:25625600-25626000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr18:25625600-25626000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr18:25625600-25626000	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr18:25625600-25626200	Flanking Active TSS	NH-A	brain
36	chr18:25625800-25626000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr18:25625800-25626000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr18:25625800-25628400	Weak transcription	Liver	Liver
39	chr18:25625800-25628400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr18:25625800-25628400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr18:25625800-25628600	Weak transcription	Fetal Kidney	kidney
42	chr18:25625800-25628800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr18:25625800-25630800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr18:25625800-25643400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr18:25625800-25650400	Weak transcription	Right Atrium	heart

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