Variant report

Variant	rs12327203
Chromosome Location	chr18:29259412-29259413
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29259001..29261313-chr18:29272206..29274958,2	MCF-7	breast:
2	chr18:29257336..29259422-chr18:29266158..29267928,2	K562	blood:
3	chr18:29259339..29260872-chr18:29261230..29264110,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10048377	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10775449	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11081707	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081708	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11660271	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11664177	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12605321	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12964693	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1449082	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1551006	0.83[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap]
rs1614197	0.95[EUR][1000 genomes]
rs1979105	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs34530749	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4799589	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs718780	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8098191	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968325	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12327203	CDH2	cis	cerebellum	SCAN
rs12327203	DSC1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29253200-29262800	Weak transcription	HepG2	liver
2	chr18:29253400-29259800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:29253400-29260000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:29253600-29260400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr18:29253600-29262200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:29253600-29264200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr18:29255600-29260000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr18:29257200-29260400	Weak transcription	Fetal Brain Female	brain
9	chr18:29257200-29261600	Flanking Active TSS	GM12878-XiMat	blood
10	chr18:29257400-29259600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr18:29257400-29260400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr18:29257400-29261000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr18:29257600-29260800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr18:29257600-29261000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr18:29257800-29259800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr18:29257800-29261000	Enhancers	Gastric	stomach
17	chr18:29257800-29261600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr18:29257800-29261800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr18:29257800-29262400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr18:29257800-29262600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr18:29258000-29260400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr18:29258000-29260600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr18:29258000-29263800	Weak transcription	Thymus	Thymus
24	chr18:29258200-29260000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr18:29258200-29260200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:29258200-29260800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr18:29258200-29261600	Enhancers	NHEK	skin
28	chr18:29258200-29262000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr18:29258200-29262600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr18:29258200-29263000	Enhancers	Primary hematopoietic stem cells	blood
31	chr18:29258200-29263200	Weak transcription	Fetal Thymus	thymus
32	chr18:29258200-29263600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr18:29258200-29263800	Weak transcription	Small Intestine	intestine
34	chr18:29258400-29261000	Enhancers	Stomach Mucosa	stomach
35	chr18:29258400-29262200	Enhancers	Fetal Intestine Large	intestine
36	chr18:29258400-29262200	Enhancers	Fetal Intestine Small	intestine
37	chr18:29258400-29263200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:29258600-29259800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr18:29258600-29259800	Enhancers	NHDF-Ad	bronchial
40	chr18:29258600-29260400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr18:29258600-29261000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr18:29258600-29261000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr18:29258800-29259600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr18:29258800-29259600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr18:29258800-29259800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:29258800-29259800	Weak transcription	Right Ventricle	heart
47	chr18:29258800-29259800	Flanking Active TSS	HUVEC	blood vessel
48	chr18:29258800-29260000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr18:29258800-29260000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr18:29258800-29260000	Weak transcription	Left Ventricle	heart

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