Variant report

Variant	rs41289039
Chromosome Location	chr1:85559396-85559397
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12021868	1.00[AFR][1000 genomes]
rs12022814	1.00[AFR][1000 genomes]
rs12023751	1.00[AFR][1000 genomes]
rs12028707	1.00[AFR][1000 genomes]
rs12034359	1.00[AFR][1000 genomes]
rs12034501	1.00[AFR][1000 genomes]
rs12036276	1.00[AFR][1000 genomes]
rs12039804	1.00[AFR][1000 genomes]
rs12040408	1.00[AFR][1000 genomes]
rs12041155	1.00[AFR][1000 genomes]
rs12043409	1.00[AFR][1000 genomes]
rs12045141	1.00[AFR][1000 genomes]
rs17099217	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17121656	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17121745	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17121935	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17121978	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2305930	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2305931	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28410552	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56191061	1.00[AFR][1000 genomes]
rs57222060	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57516443	1.00[AFR][1000 genomes]
rs58068482	1.00[AFR][1000 genomes]
rs58246117	1.00[AFR][1000 genomes]
rs58604582	1.00[AFR][1000 genomes]
rs58659750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59030463	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59248240	1.00[AFR][1000 genomes]
rs60866399	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85545400-85583400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:85549800-85560600	Weak transcription	Aorta	Aorta
3	chr1:85557400-85559400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:85558000-85566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:85558000-85567000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:85558200-85560000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:85558800-85559400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:85558800-85559600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:85558800-85559600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:85558800-85560200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:85559000-85559600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:85559200-85559800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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