Variant report

Variant	rs1667271
Chromosome Location	chr18:29242292-29242293
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	KAP1	chr18:29241918-29242367	U2OS	brain:	n/a	n/a
2	CEBPB	chr18:29241964-29242357	K562	blood:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
3	KAP1	chr18:29241911-29242320	HEK293	kidney:	n/a	n/a
4	CEBPB	chr18:29241997-29242312	ECC-1	luminal epithelium:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
5	CEBPB	chr18:29242004-29242362	MCF-7	breast:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
6	CEBPB	chr18:29241981-29242319	H1-hESC	embryonic stem cell:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
7	CEBPB	chr18:29241908-29242404	MCF-7	breast:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
8	CEBPB	chr18:29241968-29242354	IMR90	lung:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
9	CEBPB	chr18:29241852-29242336	A549	lung:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
10	POLR2A	chr18:29242158-29242358	GM12878	blood:	n/a	n/a
11	CEBPB	chr18:29241796-29242353	Hela-S3	cervix:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
12	CEBPB	chr18:29241972-29242341	HepG2	liver:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
13	CEBPB	chr18:29241944-29242345	ECC-1	luminal epithelium:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161
14	CEBPB	chr18:29241889-29242341	A549	lung:	n/a	chr18:29242150-29242163 chr18:29242150-29242163 chr18:29242152-29242161 chr18:29242152-29242161 chr18:29242151-29242162 chr18:29242152-29242161

Variant related genes	Relation type
B4GALT6	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1449085	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1449086	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1667288	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1667290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1791172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1791175	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2595372	0.93[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap]
rs2852319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1667271	DSC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29219200-29252000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:29219200-29252000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr18:29227600-29252000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr18:29229200-29245200	Weak transcription	Brain Anterior Caudate	brain
5	chr18:29229400-29252800	Weak transcription	NHEK	skin
6	chr18:29231200-29242400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr18:29231800-29251800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr18:29235600-29254800	Weak transcription	HUVEC	blood vessel
9	chr18:29235600-29257800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:29237400-29243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:29238400-29247000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr18:29239000-29252000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr18:29239200-29244400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr18:29239200-29252200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr18:29239400-29252200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr18:29239600-29245200	Weak transcription	Placenta	Placenta
17	chr18:29239600-29249200	Weak transcription	Dnd41	blood
18	chr18:29239600-29252000	Weak transcription	Adipose Nuclei	Adipose
19	chr18:29239600-29252600	Weak transcription	Fetal Muscle Leg	muscle
20	chr18:29239600-29253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:29239600-29258000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr18:29239800-29243600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr18:29239800-29249800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr18:29239800-29252800	Weak transcription	Fetal Thymus	thymus
25	chr18:29240000-29243800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr18:29240000-29243800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr18:29240000-29249200	Weak transcription	Fetal Intestine Large	intestine
28	chr18:29240200-29245000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr18:29240400-29247000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr18:29240800-29244200	ZNF genes & repeats	GM12878-XiMat	blood
31	chr18:29241000-29242400	Enhancers	Fetal Lung	lung
32	chr18:29241200-29243800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr18:29241200-29244400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr18:29241200-29246000	Weak transcription	Fetal Kidney	kidney
35	chr18:29241200-29252600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr18:29241200-29253200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr18:29241400-29243000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr18:29241400-29244200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr18:29241600-29242400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr18:29241600-29243200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:29241800-29242400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr18:29241800-29242400	Enhancers	NH-A	brain
43	chr18:29241800-29242600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr18:29241800-29242600	Enhancers	Osteobl	bone
45	chr18:29241800-29244600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr18:29242000-29242400	Enhancers	Fetal Intestine Small	intestine
47	chr18:29242000-29242600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:29242200-29242400	Enhancers	A549	lung
49	chr18:29242200-29242600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr18:29242200-29247000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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