Variant report

Variant	rs1966488
Chromosome Location	chr5:167738942-167738943
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:35311075..35312996-chr5:167737118..167739327,2	MCF-7	breast:
2	chr5:167738439..167740014-chr5:167740372..167743298,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12522354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12522956	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13183480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17775705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17832301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2112556	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337215	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34509932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35397127	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59173424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949154	chr5:167691208-168323234	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv5119	chr5:167724987-167766076	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167727600-167742600	Weak transcription	Fetal Brain Female	brain
2	chr5:167729400-167740800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:167729400-167741000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:167729400-167741000	Weak transcription	Fetal Lung	lung
5	chr5:167730400-167740800	Weak transcription	HMEC	breast
6	chr5:167730800-167740800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:167731000-167739200	Weak transcription	Hela-S3	cervix
8	chr5:167731000-167741600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:167733000-167740800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:167734200-167740800	Weak transcription	NHEK	skin
11	chr5:167734200-167746000	Enhancers	Fetal Intestine Large	intestine
12	chr5:167734400-167746600	Enhancers	Fetal Intestine Small	intestine
13	chr5:167736200-167739400	Weak transcription	Small Intestine	intestine
14	chr5:167736400-167740000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:167736400-167741600	Enhancers	Liver	Liver
16	chr5:167736600-167740600	Enhancers	Duodenum Mucosa	Duodenum
17	chr5:167736600-167741000	Genic enhancers	A549	lung
18	chr5:167736800-167739600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:167737200-167739400	Weak transcription	NHDF-Ad	bronchial
20	chr5:167738200-167739400	Weak transcription	Brain Anterior Caudate	brain
21	chr5:167738200-167740800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:167738200-167740800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:167738200-167741000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:167738200-167741600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:167738200-167741600	Weak transcription	Fetal Kidney	kidney
26	chr5:167738200-167742200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:167738200-167747600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:167738400-167739400	Weak transcription	HepG2	liver
29	chr5:167738400-167739800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:167738400-167740200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:167738400-167740200	Weak transcription	NH-A	brain
32	chr5:167738400-167740800	Weak transcription	Placenta	Placenta
33	chr5:167738400-167740800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:167738400-167741000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:167738400-167741000	Weak transcription	Gastric	stomach
36	chr5:167738400-167741000	Weak transcription	Lung	lung
37	chr5:167738400-167741600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:167738400-167741600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:167738400-167744400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr5:167738600-167739400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:167738600-167739600	Weak transcription	Pancreas	Pancrea
42	chr5:167738600-167740200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:167738600-167740200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:167738600-167740800	Weak transcription	Stomach Mucosa	stomach
45	chr5:167738600-167741000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:167738600-167741600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:167738600-167741800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr5:167738800-167739200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links