Variant report

Variant	rs17446644
Chromosome Location	chr18:25694712-25694713
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11564386	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1231234	0.88[YRI][hapmap]
rs1231238	0.80[YRI][hapmap]
rs1639387	0.80[YRI][hapmap]
rs17446484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17446616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17446875	1.00[CHB][hapmap]
rs17469008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17494961	1.00[YRI][hapmap]
rs1789464	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2155765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2155766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2628604	0.80[YRI][hapmap]
rs28564564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716460	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8094132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961497	0.80[YRI][hapmap]
rs9946601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9956424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17446644	CDH2	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25687200-25699800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr18:25687400-25696800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr18:25689800-25695600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr18:25690200-25695000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr18:25690200-25695000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr18:25690800-25695200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr18:25691000-25696600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:25691200-25695000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr18:25691200-25695000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr18:25691200-25695200	Weak transcription	Right Atrium	heart
11	chr18:25691400-25695000	Weak transcription	Left Ventricle	heart
12	chr18:25691400-25696800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr18:25691400-25703400	Weak transcription	Fetal Brain Male	brain
14	chr18:25691600-25695600	Enhancers	NHEK	skin
15	chr18:25692200-25703200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr18:25692400-25695000	Weak transcription	Brain Angular Gyrus	brain
17	chr18:25692400-25695000	Weak transcription	Hela-S3	cervix
18	chr18:25692400-25695000	Enhancers	HSMM	muscle
19	chr18:25692400-25696600	Enhancers	HUVEC	blood vessel
20	chr18:25692800-25694800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr18:25692800-25695000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:25692800-25695000	Weak transcription	Aorta	Aorta
23	chr18:25692800-25695200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr18:25692800-25695600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr18:25692800-25696800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr18:25692800-25699600	Weak transcription	Brain Substantia Nigra	brain
27	chr18:25692800-25700600	Enhancers	Fetal Heart	heart
28	chr18:25692800-25703600	Weak transcription	Ovary	ovary
29	chr18:25693000-25694800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr18:25693000-25694800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:25693000-25694800	Weak transcription	Liver	Liver
32	chr18:25693000-25695000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr18:25693000-25695000	Weak transcription	Brain Anterior Caudate	brain
34	chr18:25693000-25696000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr18:25693000-25697400	Weak transcription	Brain Germinal Matrix	brain
36	chr18:25693000-25699200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr18:25693200-25695000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr18:25693200-25695000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr18:25693200-25703600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr18:25693600-25696000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr18:25693800-25696200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr18:25694000-25695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr18:25694000-25695200	Flanking Active TSS	NH-A	brain
44	chr18:25694000-25695600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr18:25694000-25695600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr18:25694000-25696800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr18:25694200-25695000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr18:25694200-25696200	Enhancers	HSMMtube	muscle
49	chr18:25694200-25696400	Enhancers	NHLF	lung
50	chr18:25694400-25694800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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