Variant report

Variant	rs28627760
Chromosome Location	chr4:78985571-78985572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10016219	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016229	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016432	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1502882	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036454	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055493	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28733880	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334779	0.84[AMR][1000 genomes]
rs4591635	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4597857	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4615194	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4642273	0.81[AMR][1000 genomes]
rs4859907	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859909	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859912	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7659437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689647	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs873453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs873454	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs873455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78980800-78990000	Weak transcription	NHDF-Ad	bronchial
2	chr4:78980800-78990600	Weak transcription	Psoas Muscle	Psoas
3	chr4:78980800-78998200	Weak transcription	Pancreas	Pancrea
4	chr4:78981000-78990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:78981000-78991200	Weak transcription	Right Atrium	heart
6	chr4:78981000-78995600	Weak transcription	Fetal Intestine Small	intestine
7	chr4:78981200-79016600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:78981400-78986600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:78981400-78990400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:78981600-78986600	Weak transcription	Fetal Intestine Large	intestine
11	chr4:78981800-78986600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:78981800-78987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:78982200-78990600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:78982200-78998200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:78983400-78996000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:78983400-79001000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:78984000-78990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:78984200-78991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:78984400-78986800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:78984600-78986000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:78984600-78986400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:78984600-78990600	Weak transcription	HMEC	breast
23	chr4:78984800-78986000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:78984800-78986600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:78984800-78986600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:78984800-78986600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:78984800-78986600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:78984800-78986600	Weak transcription	HepG2	liver
29	chr4:78985400-78986600	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links