Variant report

Variant	rs72833431
Chromosome Location	chr2:113101104-113101105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113080011..113082440-chr2:113099330..113101627,2	K562	blood:
2	chr2:113031545..113034339-chr2:113100892..113102662,2	MCF-7	breast:
3	chr2:113059563..113061506-chr2:113099982..113102313,2	K562	blood:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10167748	0.80[AFR][1000 genomes]
rs10191002	0.84[AFR][1000 genomes]
rs10864901	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11123133	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11679986	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11682795	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11685462	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11685514	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11687980	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11688511	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11689858	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11693294	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11695974	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12474447	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12477879	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13387611	0.86[AFR][1000 genomes]
rs4507112	0.86[AFR][1000 genomes]
rs4516428	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4522611	0.80[AFR][1000 genomes]
rs4525706	0.86[AFR][1000 genomes]
rs4622729	0.80[AFR][1000 genomes]
rs55798617	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55802705	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55821286	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55861985	0.88[EUR][1000 genomes]
rs56044884	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56048537	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58360798	0.83[EUR][1000 genomes]
rs6542052	0.81[AFR][1000 genomes]
rs6542053	0.84[AFR][1000 genomes]
rs6708164	0.80[AFR][1000 genomes]
rs6711180	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6722612	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6733138	0.86[AFR][1000 genomes]
rs6744364	0.86[AFR][1000 genomes]
rs6747639	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6751146	0.86[AFR][1000 genomes]
rs6758110	0.86[AFR][1000 genomes]
rs6759283	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6761599	0.86[AFR][1000 genomes]
rs72831641	0.81[AMR][1000 genomes]
rs72831642	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72831649	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831651	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831658	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831660	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831662	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72831664	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72831685	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72831688	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833410	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833412	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833413	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833414	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833415	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72833428	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72833432	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7557862	0.86[AFR][1000 genomes]
rs7569894	0.80[AFR][1000 genomes]
rs7586893	0.81[AMR][1000 genomes]
rs7587316	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7591439	0.86[AFR][1000 genomes]
rs7596661	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7599041	0.86[AFR][1000 genomes]
rs7599551	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs72833431	RGPD8	cis	Heart Left Ventricle	GTEx
rs72833431	RGPD8	cis	lung	GTEx
rs72833431	RGPD8	cis	Artery Tibial	GTEx
rs72833431	RGPD8	cis	Adipose Subcutaneous	GTEx
rs72833431	RGPD8	cis	Esophagus Mucosa	GTEx
rs72833431	RGPD8	cis	Esophagus Muscularis	GTEx
rs72833431	RGPD8	cis	Thyroid	GTEx
rs72833431	RGPD8	cis	Whole Blood	GTEx
rs72833431	ZC3H8	cis	Artery Tibial	GTEx
rs72833431	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs72833431	RGPD8	cis	Muscle Skeletal	GTEx
rs72833431	RGPD8	cis	Nerve Tibial	GTEx
rs72833431	RGPD8	cis	Artery Aorta	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113068200-113101400	Weak transcription	NHDF-Ad	bronchial
2	chr2:113085800-113103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:113089400-113103400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:113089600-113101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:113089600-113101400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:113090000-113101200	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:113090000-113101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:113090000-113103400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:113090000-113103400	Weak transcription	Spleen	Spleen
10	chr2:113096800-113101400	Enhancers	Fetal Intestine Large	intestine
11	chr2:113097400-113101600	Weak transcription	HepG2	liver
12	chr2:113098400-113104400	Weak transcription	Fetal Kidney	kidney
13	chr2:113100600-113102600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:113100800-113102400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr2:113101000-113101400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:113101000-113102400	Enhancers	Adipose Nuclei	Adipose

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