Variant report

Variant	rs2919999
Chromosome Location	chr18:28784342-28784343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:28781545..28784523-chr18:28786005..28788278,2	MCF-7	breast:
2	chr18:28783058..28785177-chr18:28785602..28787795,2	K562	blood:
3	chr18:28781990..28784653-chr18:28785130..28789773,4	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1365296	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs1469300	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469301	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469302	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469304	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469945	0.92[CEU][hapmap];0.85[GIH][hapmap]
rs2011596	0.92[EUR][1000 genomes]
rs2162275	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2912328	0.96[EUR][1000 genomes]
rs2919996	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs2919998	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6506895	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506896	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2919999	KLHL14	cis	parietal	SCAN
rs2919999	DSC1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28771000-28789000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:28779800-28786200	Weak transcription	Hela-S3	cervix
3	chr18:28780000-28788400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr18:28780200-28786800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr18:28782600-28787600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr18:28783200-28784400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:28783200-28787200	Active TSS	Duodenum Mucosa	Duodenum
8	chr18:28783400-28784800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr18:28783400-28785200	Enhancers	A549	lung
10	chr18:28783400-28786600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr18:28783400-28791200	Weak transcription	Right Ventricle	heart
12	chr18:28783600-28784800	Weak transcription	Pancreas	Pancrea
13	chr18:28783600-28784800	Weak transcription	K562	blood
14	chr18:28783600-28786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr18:28783600-28786800	Enhancers	Primary B cells from cord blood	blood
16	chr18:28783800-28784600	Weak transcription	Right Atrium	heart
17	chr18:28783800-28784800	Weak transcription	Placenta	Placenta
18	chr18:28783800-28784800	Weak transcription	Left Ventricle	heart
19	chr18:28783800-28784800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr18:28783800-28786400	Weak transcription	HMEC	breast
21	chr18:28783800-28786800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:28784000-28784600	Weak transcription	Stomach Mucosa	stomach
23	chr18:28784000-28784800	Weak transcription	Fetal Intestine Small	intestine
24	chr18:28784000-28784800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr18:28784000-28785000	Weak transcription	Colonic Mucosa	Colon
26	chr18:28784000-28785000	Enhancers	HepG2	liver
27	chr18:28784000-28785800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr18:28784000-28786000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr18:28784000-28786200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr18:28784000-28786400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:28784000-28786400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr18:28784000-28786400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr18:28784000-28786600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr18:28784000-28786800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr18:28784000-28786800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr18:28784000-28787000	Weak transcription	Fetal Lung	lung
37	chr18:28784000-28787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr18:28784000-28789000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:28784200-28784400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr18:28784200-28784600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr18:28784200-28784600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:28784200-28784600	Weak transcription	Liver	Liver
43	chr18:28784200-28784600	Weak transcription	Esophagus	oesophagus
44	chr18:28784200-28784600	Weak transcription	Fetal Heart	heart
45	chr18:28784200-28784600	Weak transcription	Fetal Intestine Large	intestine
46	chr18:28784200-28784600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr18:28784200-28786000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr18:28784200-28786000	Enhancers	NHEK	skin

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