Variant report

Variant	rs1449077
Chromosome Location	chr18:29129060-29129061
allele	G/T
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:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1042769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11661247	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12326068	0.90[CEU][hapmap];0.99[EUR][1000 genomes]
rs1626261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1791174	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941939	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096919	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276150	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2704039	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2704041	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2848664	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28522238	0.91[EUR][1000 genomes]
rs6506931	0.92[EUR][1000 genomes]
rs8084771	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs9304100	0.81[EUR][1000 genomes]
rs9304101	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs9947401	0.90[CEU][hapmap];0.99[EUR][1000 genomes]
rs9949695	0.88[EUR][1000 genomes]
rs9949790	0.88[EUR][1000 genomes]
rs9951860	0.91[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1449077	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:50 , 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	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
3	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
5	chr18:29117000-29136000	Weak transcription	A549	lung
6	chr18:29120000-29129600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:29122800-29131800	Weak transcription	Colonic Mucosa	Colon
8	chr18:29123400-29129800	Weak transcription	Adipose Nuclei	Adipose
9	chr18:29123600-29131200	Weak transcription	Placenta	Placenta
10	chr18:29123600-29142200	Weak transcription	Fetal Kidney	kidney
11	chr18:29126600-29131000	Weak transcription	Liver	Liver
12	chr18:29126600-29132800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr18:29126600-29133800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:29126600-29136200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr18:29126800-29129600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr18:29126800-29136000	Weak transcription	GM12878-XiMat	blood
17	chr18:29126800-29136200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr18:29127000-29136200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr18:29127200-29131600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:29127200-29131600	Weak transcription	Fetal Lung	lung
21	chr18:29127200-29136000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr18:29127200-29136200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr18:29127200-29136200	Weak transcription	Ovary	ovary
24	chr18:29127200-29136200	Weak transcription	Hela-S3	cervix
25	chr18:29127400-29129200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr18:29127400-29129600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr18:29127400-29129600	Weak transcription	HMEC	breast
28	chr18:29127400-29131200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr18:29127400-29132600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr18:29127400-29136000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr18:29127600-29136000	Weak transcription	NHEK	skin
32	chr18:29127600-29136200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr18:29128000-29129600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr18:29128000-29131600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr18:29128000-29133800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr18:29128400-29129400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr18:29128400-29129800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr18:29128600-29129800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr18:29128600-29130200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr18:29128800-29129800	Enhancers	Fetal Intestine Small	intestine
41	chr18:29129000-29129200	Enhancers	Duodenum Mucosa	Duodenum
42	chr18:29129000-29129200	Enhancers	Gastric	stomach
43	chr18:29129000-29129400	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr18:29129000-29129600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr18:29129000-29129600	Enhancers	HepG2	liver
46	chr18:29129000-29129800	Enhancers	Fetal Intestine Large	intestine
47	chr18:29129000-29129800	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr18:29129000-29129800	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr18:29129000-29130000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr18:29129000-29130400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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