Variant report

Variant	rs1449086
Chromosome Location	chr18:29237765-29237766
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29235239..29238459-chr18:29263541..29266170,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118276	Chromatin interaction
ENSG00000259985	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1449085	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1449087	0.80[ASN][1000 genomes]
rs1667271	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];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1667290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1791172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1791175	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2595372	0.93[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2852319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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
rs1449086	DSC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29202800-29240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr18:29204600-29238600	Weak transcription	Gastric	stomach
3	chr18:29219200-29240000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:29219200-29252000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:29219200-29252000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr18:29227400-29238000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr18:29227600-29252000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr18:29227800-29238800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr18:29227800-29240800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:29228600-29238000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr18:29229200-29238200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:29229200-29238200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr18:29229200-29245200	Weak transcription	Brain Anterior Caudate	brain
14	chr18:29229400-29238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:29229400-29239600	Weak transcription	Brain Hippocampus Middle	brain
16	chr18:29229400-29239600	Weak transcription	Right Atrium	heart
17	chr18:29229400-29252800	Weak transcription	NHEK	skin
18	chr18:29229600-29238200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:29229600-29239800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:29230600-29238200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr18:29231000-29238200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:29231200-29242400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr18:29231800-29251800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr18:29233000-29239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:29233200-29237800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr18:29233200-29238800	Weak transcription	Fetal Thymus	thymus
27	chr18:29233400-29237800	Weak transcription	Primary B cells from cord blood	blood
28	chr18:29233400-29238200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr18:29233400-29238600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr18:29234400-29238600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr18:29235200-29238000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr18:29235400-29237800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr18:29235600-29239000	Weak transcription	Fetal Brain Female	brain
34	chr18:29235600-29254800	Weak transcription	HUVEC	blood vessel
35	chr18:29235600-29257800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr18:29236000-29237800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr18:29236400-29239200	Weak transcription	Small Intestine	intestine
38	chr18:29236800-29237800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr18:29236800-29238000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr18:29236800-29238400	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr18:29237000-29240000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr18:29237000-29240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr18:29237200-29238200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr18:29237400-29237800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr18:29237400-29239800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr18:29237400-29240000	Enhancers	Fetal Intestine Small	intestine
47	chr18:29237400-29243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr18:29237600-29238000	Weak transcription	Fetal Intestine Large	intestine
49	chr18:29237600-29239600	Strong transcription	Dnd41	blood
50	chr18:29237600-29240000	Flanking Active TSS	GM12878-XiMat	blood

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