Variant report

Variant	rs1667216
Chromosome Location	chr18:29129931-29129932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29089738..29092422-chr18:29128090..29130094,2	MCF-7	breast:
2	chr18:29129102..29131935-chr18:29134564..29137415,2	K562	blood:

Variant related genes	Relation type
ENSG00000264859	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1047433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449078	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667218	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1791173	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1791176	0.81[EUR][1000 genomes]
rs1791230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1791233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1791235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941938	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2155948	0.82[GIH][hapmap]
rs2230233	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2276149	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs2595364	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2704038	0.94[EUR][1000 genomes]
rs2704042	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs28376849	0.86[EUR][1000 genomes]
rs3108921	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3132910	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7243604	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv576635	chr18:29129931-29148814	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1667216	DSG4	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
4	chr18:29117000-29136000	Weak transcription	A549	lung
5	chr18:29122800-29131800	Weak transcription	Colonic Mucosa	Colon
6	chr18:29123600-29131200	Weak transcription	Placenta	Placenta
7	chr18:29123600-29142200	Weak transcription	Fetal Kidney	kidney
8	chr18:29126600-29131000	Weak transcription	Liver	Liver
9	chr18:29126600-29132800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr18:29126600-29133800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:29126600-29136200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr18:29126800-29136000	Weak transcription	GM12878-XiMat	blood
13	chr18:29126800-29136200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr18:29127000-29136200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr18:29127200-29131600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr18:29127200-29131600	Weak transcription	Fetal Lung	lung
17	chr18:29127200-29136000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr18:29127200-29136200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr18:29127200-29136200	Weak transcription	Ovary	ovary
20	chr18:29127200-29136200	Weak transcription	Hela-S3	cervix
21	chr18:29127400-29131200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr18:29127400-29132600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr18:29127400-29136000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr18:29127600-29136000	Weak transcription	NHEK	skin
25	chr18:29127600-29136200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr18:29128000-29131600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr18:29128000-29133800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr18:29128600-29130200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr18:29129000-29130000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr18:29129000-29130400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr18:29129200-29143200	Weak transcription	Gastric	stomach
32	chr18:29129400-29131200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr18:29129600-29130000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr18:29129600-29130400	Strong transcription	HMEC	breast
35	chr18:29129600-29130800	Weak transcription	HepG2	liver
36	chr18:29129800-29130000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr18:29129800-29131000	Weak transcription	Fetal Intestine Large	intestine
38	chr18:29129800-29131800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr18:29129800-29134200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr18:29129800-29134200	Weak transcription	Fetal Intestine Small	intestine

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