Variant report

Variant	rs28208
Chromosome Location	chr5:106813191-106813192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106804269..106806001-chr5:106811560..106813893,2	MCF-7	breast:
2	chr5:106812320..106814965-chr5:107717200..107719891,2	K562	blood:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs25740	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs25964	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs25965	0.83[ASN][1000 genomes]
rs26241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26243	0.82[ASN][1000 genomes]
rs26244	0.82[ASN][1000 genomes]
rs27929	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28024	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28112	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29543	0.87[AFR][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	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106802600-106813600	Weak transcription	Right Ventricle	heart
2	chr5:106805600-106822600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:106806000-106825600	Weak transcription	Aorta	Aorta
4	chr5:106806200-106813400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:106806200-106813600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:106806200-106822200	Weak transcription	HSMM	muscle
7	chr5:106806400-106813800	Weak transcription	NHDF-Ad	bronchial
8	chr5:106806800-106815600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:106808400-106813200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr5:106808400-106837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:106808600-106813800	Weak transcription	Esophagus	oesophagus
12	chr5:106808600-106822600	Weak transcription	Gastric	stomach
13	chr5:106808800-106813800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:106808800-106822800	Weak transcription	Left Ventricle	heart
15	chr5:106809000-106822800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:106809200-106814800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr5:106809400-106814000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr5:106809800-106814600	Enhancers	HUVEC	blood vessel
19	chr5:106810000-106814200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:106810000-106814400	Enhancers	Fetal Heart	heart
21	chr5:106810200-106813600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:106810200-106814200	Enhancers	GM12878-XiMat	blood
23	chr5:106810400-106817800	Weak transcription	Right Atrium	heart
24	chr5:106811000-106813800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr5:106811200-106814000	Weak transcription	Placenta	Placenta
26	chr5:106811200-106816800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:106811400-106814000	Weak transcription	Fetal Kidney	kidney
28	chr5:106811400-106817200	Weak transcription	Small Intestine	intestine
29	chr5:106811600-106813600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:106811600-106813800	Weak transcription	Fetal Intestine Small	intestine
31	chr5:106811600-106819200	Weak transcription	Fetal Lung	lung
32	chr5:106812000-106815400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:106812000-106815400	Enhancers	NHEK	skin
34	chr5:106812000-106816000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr5:106812200-106813200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:106812200-106813600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr5:106812200-106813800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:106812200-106814200	Enhancers	Duodenum Mucosa	Duodenum
39	chr5:106812200-106814600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:106812200-106814600	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr5:106812200-106814800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:106812200-106815000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr5:106812200-106815800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr5:106812200-106816200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:106812400-106813400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:106812400-106813400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:106812400-106813600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr5:106812400-106813800	Enhancers	Hela-S3	cervix
49	chr5:106812400-106814400	Enhancers	Fetal Intestine Large	intestine
50	chr5:106812400-106814600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links