Variant report

Variant	rs1715554
Chromosome Location	chr3:102399856-102399857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11708911	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11720453	0.97[ASN][1000 genomes]
rs12486666	0.80[ASN][1000 genomes]
rs12495176	0.85[ASN][1000 genomes]
rs1354727	1.00[ASN][1000 genomes]
rs1391422	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1391423	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474186	1.00[ASN][1000 genomes]
rs1498081	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498086	0.80[ASN][1000 genomes]
rs1506436	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581303	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1581304	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1589287	0.97[ASN][1000 genomes]
rs1599776	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1609976	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1715542	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1715546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1715547	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1715553	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17831612	0.82[EUR][1000 genomes]
rs2088475	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2971239	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34116120	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4241417	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4383531	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4856111	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4856112	0.95[ASN][1000 genomes]
rs4856130	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4856149	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55635554	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6441670	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441671	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6764453	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6768201	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6768503	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6770963	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73137703	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73137731	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73137742	0.82[EUR][1000 genomes]
rs73139703	0.82[EUR][1000 genomes]
rs73139709	0.82[EUR][1000 genomes]
rs7355983	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636527	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639003	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650400	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9290744	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939326	1.00[ASN][1000 genomes]
rs9810913	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9844846	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869638	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007340	chr3:102108954-102725099	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv536676	chr3:102108954-102725099	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1009392	chr3:102199756-102631205	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv877228	chr3:102345638-102751470	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv591190	chr3:102345638-102946216	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834776	chr3:102351486-102532042	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1000584	chr3:102358773-102923378	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv915978	chr3:102386795-102949530	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:102393000-102406400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:102399200-102400000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr3:102399200-102401000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:102399400-102400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:102399400-102403000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:102399400-102404800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:102399400-102405400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:102399400-102405600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:102399400-102406200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links