Variant report

Variant	rs3806230
Chromosome Location	chr1:153284782-153284783
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	chr1:153284760..153285743-chr1:153325777..153326381,2	MCF-7	breast:
2	chr1:153274688..153277090-chr1:153283483..153285851,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGLYRP4-1	chr1:153284290-153303044	predAs_engstrom06_CR598625_1

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10888551	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11589286	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139503	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1897695	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117130	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288990	0.96[ASN][1000 genomes]
rs2916220	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916223	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2916224	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916225	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916226	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916227	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916228	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916229	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916230	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916231	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2916232	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916233	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2916235	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916236	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987759	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987760	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987763	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987764	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987766	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987767	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987768	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987769	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3006411	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006427	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006431	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006434	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006439	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006440	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006441	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006444	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006445	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006446	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006447	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006472	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006473	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3014853	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3014854	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3014855	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3014858	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3125234	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753460	0.93[ASN][1000 genomes]
rs9435978	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9435979	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9435983	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436076	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436077	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436084	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs957195	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9661293	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9970937	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv999024	chr1:153255005-153325685	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153280400-153285200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:153283400-153284800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:153284600-153285000	Weak transcription	Esophagus	oesophagus
4	chr1:153284600-153285200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:153284600-153285200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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