Variant report

Variant	rs1028000
Chromosome Location	chr4:54460531-54460532
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	chr4:54460125..54463943-chr4:54465847..54469777,4	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10009930	0.85[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1965112	0.81[CHD][hapmap]
rs925477	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv437918	chr4:54451175-54483569	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879014	chr4:54451246-54461548	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54457600-54464400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:54459000-54460800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:54459400-54462400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:54459600-54463400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:54459600-54465000	Weak transcription	Osteobl	bone
6	chr4:54459600-54465200	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:54459600-54465200	Weak transcription	Right Ventricle	heart
8	chr4:54459600-54465400	Weak transcription	Left Ventricle	heart
9	chr4:54459600-54467400	Weak transcription	Esophagus	oesophagus
10	chr4:54459600-54467400	Weak transcription	Pancreas	Pancrea
11	chr4:54459600-54467400	Weak transcription	Right Atrium	heart
12	chr4:54459800-54460800	Enhancers	Fetal Intestine Large	intestine
13	chr4:54459800-54461200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:54459800-54461200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:54459800-54464200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:54459800-54464600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:54459800-54464600	Weak transcription	Stomach Mucosa	stomach
18	chr4:54459800-54467400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:54460000-54460800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr4:54460000-54465800	Weak transcription	GM12878-XiMat	blood
21	chr4:54460200-54461200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:54460200-54461200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:54460200-54461200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:54460200-54461200	Weak transcription	HMEC	breast
25	chr4:54460200-54461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:54460200-54461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:54460200-54461600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:54460200-54461800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr4:54460200-54461800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:54460200-54464600	Weak transcription	Fetal Intestine Small	intestine
31	chr4:54460200-54467400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:54460200-54467400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:54460200-54467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:54460400-54460600	Enhancers	Placenta	Placenta
35	chr4:54460400-54460800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:54460400-54462200	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links