Variant report

Variant	rs542149
Chromosome Location	chr1:168689511-168689512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168687992..168690968-chr1:169074468..169076172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs512129	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs523447	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs524705	0.81[JPT][hapmap]
rs528953	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs529949	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531706	0.96[ASN][1000 genomes]
rs533619	0.96[ASN][1000 genomes]
rs534503	0.82[ASN][1000 genomes]
rs544013	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs545833	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs573418	0.96[ASN][1000 genomes]
rs581753	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs590033	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs590875	0.96[ASN][1000 genomes]
rs607484	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs627406	0.81[JPT][hapmap]
rs631451	0.81[JPT][hapmap]
rs635954	0.96[ASN][1000 genomes]
rs6427145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678629	0.96[ASN][1000 genomes]
rs686226	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv831847	chr1:168669877-168850129	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168678200-168695600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:168679200-168694600	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:168679600-168694600	Weak transcription	Fetal Stomach	stomach
4	chr1:168679800-168694600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:168680200-168694800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:168681400-168692400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:168683600-168696000	Weak transcription	Left Ventricle	heart
8	chr1:168687000-168689600	Strong transcription	Adipose Nuclei	Adipose
9	chr1:168687200-168689600	Enhancers	HMEC	breast
10	chr1:168687600-168689600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:168687600-168692200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:168687600-168695000	Weak transcription	Fetal Lung	lung
13	chr1:168688000-168691000	Weak transcription	Right Atrium	heart
14	chr1:168688000-168695200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:168688200-168689600	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:168688200-168692200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:168688200-168694800	Enhancers	Fetal Heart	heart
18	chr1:168688400-168689600	Enhancers	HepG2	liver
19	chr1:168689000-168692200	Weak transcription	Pancreas	Pancrea
20	chr1:168689000-168697000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:168689200-168690000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:168689400-168694200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links