Variant report

Variant	rs259568
Chromosome Location	chr3:22004297-22004298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10440125	0.84[AFR][1000 genomes]
rs11706252	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs12638980	0.84[AFR][1000 genomes]
rs13061226	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs13095013	0.83[AFR][1000 genomes]
rs1383073	0.84[AFR][1000 genomes]
rs1391330	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs1391331	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs1479962	0.84[AFR][1000 genomes]
rs1479963	0.84[AFR][1000 genomes]
rs1479964	0.84[AFR][1000 genomes]
rs1479965	0.83[AFR][1000 genomes]
rs1479966	0.93[YRI][hapmap]
rs1479968	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs1479969	0.83[AFR][1000 genomes]
rs1486332	0.82[AFR][1000 genomes]
rs1486333	0.93[YRI][hapmap]
rs1486372	0.84[AFR][1000 genomes]
rs1497938	0.83[AFR][1000 genomes]
rs1497939	0.81[AFR][1000 genomes]
rs1684495	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs1694042	0.83[AFR][1000 genomes]
rs1842308	0.83[AFR][1000 genomes]
rs1842309	0.83[AFR][1000 genomes]
rs1846165	0.83[AFR][1000 genomes]
rs1846166	0.93[YRI][hapmap]
rs2061938	0.83[AFR][1000 genomes]
rs2061939	0.83[AFR][1000 genomes]
rs2061940	0.83[AFR][1000 genomes]
rs2127523	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs259565	1.00[EUR][1000 genomes]
rs259567	1.00[EUR][1000 genomes]
rs259570	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3821386	0.80[AFR][1000 genomes]
rs3821388	0.83[AFR][1000 genomes]
rs3821389	0.83[AFR][1000 genomes]
rs3821390	0.84[AFR][1000 genomes]
rs3821392	0.82[AFR][1000 genomes]
rs3821394	0.82[AFR][1000 genomes]
rs4348015	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs475648	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs555679	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs555719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs555888	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs647468	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6550648	0.84[EUR][1000 genomes]
rs676651	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6786704	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6789283	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6790810	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7433115	0.81[AFR][1000 genomes]
rs7652410	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9809089	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs9809324	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs9810225	0.83[AFR][1000 genomes]
rs9811248	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs9811419	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs9816540	0.83[AFR][1000 genomes]
rs9821571	0.83[AFR][1000 genomes]
rs9821707	0.83[AFR][1000 genomes]
rs9821722	0.83[AFR][1000 genomes]
rs9821912	0.83[AFR][1000 genomes]
rs9822011	0.83[AFR][1000 genomes]
rs9828376	0.84[AFR][1000 genomes]
rs9828689	0.84[AFR][1000 genomes]
rs9834671	0.84[AFR][1000 genomes]
rs9841763	0.83[AFR][1000 genomes]
rs9859355	0.83[AFR][1000 genomes]
rs9873106	0.83[AFR][1000 genomes]
rs9873232	0.83[AFR][1000 genomes]
rs9879858	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751992	chr3:21786893-22212357	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv948555	chr3:21786893-22212357	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1003085	chr3:21887971-22415107	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv834633	chr3:21918264-22088338	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv876616	chr3:21946847-22310622	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv876617	chr3:21955784-22310622	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv999478	chr3:21971861-22012241	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv1000732	chr3:21976969-22012241	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv1007663	chr3:21984364-22022923	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv1014467	chr3:21985380-22008097	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	nsv1014852	chr3:21985380-22010086	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	nsv1012249	chr3:21985380-22012241	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	nsv1009404	chr3:21985380-22018041	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
14	nsv1001030	chr3:21985380-22022923	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
15	nsv460474	chr3:21985417-22047934	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv589932	chr3:21985417-22047934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
17	nsv1007886	chr3:21985691-22018041	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	nsv998319	chr3:21999480-22033364	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
19	nsv432404	chr3:22000296-22433396	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs259568	HMGB1P5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:22003000-22004600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:22003400-22004800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:22003400-22004800	Enhancers	Fetal Stomach	stomach
4	chr3:22003600-22004400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:22003600-22004600	Enhancers	Liver	Liver
6	chr3:22003600-22004800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:22003600-22005000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:22003800-22004600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:22003800-22004600	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr3:22003800-22004800	Enhancers	NH-A	brain
11	chr3:22004000-22004600	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links