Variant report

Variant	rs3925517
Chromosome Location	chr5:178072334-178072335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178051814..178054054-chr5:178071532..178073696,2	MCF-7	breast:
2	chr5:178063341..178065728-chr5:178071679..178073201,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10035569	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10063148	0.96[CEU][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10066600	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10070146	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10070856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464049	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10464070	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10479431	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10479500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11747899	0.82[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs12054903	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12188543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12189095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13181921	0.84[ASN][1000 genomes]
rs2045892	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs262029	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs34724127	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34893037	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35178365	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35604659	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35943178	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3925518	0.82[CEU][hapmap]
rs4424014	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4437395	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4579274	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976738	0.85[CEU][hapmap]
rs543862	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs55724549	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55783860	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57862544	0.87[ASN][1000 genomes]
rs62392801	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6883747	0.82[CEU][hapmap]
rs6884172	0.85[ASN][1000 genomes]
rs6884657	0.85[ASN][1000 genomes]
rs71611451	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71611452	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7700943	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs7724406	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs9329047	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1023697	chr5:178070594-178126328	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537972	chr5:178070594-178126328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3925517	ARL10	cis	cerebellum	SCAN
rs3925517	RUFY1	cis	parietal	SCAN
rs3925517	PROP1	cis	cerebellum	SCAN
rs3925517	FLT4	cis	parietal	SCAN
rs3925517	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs3925517	CLK4	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178067600-178072400	Enhancers	Osteobl	bone
2	chr5:178070200-178078000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:178071200-178072600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:178071200-178072600	Enhancers	HMEC	breast
5	chr5:178071400-178072600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:178071400-178072600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr5:178071600-178072400	Enhancers	NHDF-Ad	bronchial
8	chr5:178071600-178072400	Enhancers	NHEK	skin
9	chr5:178071600-178072600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:178071600-178072600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:178071600-178072600	Enhancers	HUVEC	blood vessel
12	chr5:178072000-178072400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:178072000-178072400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:178072000-178072400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:178072000-178072400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:178072000-178072400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:178072200-178072600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:178072200-178072600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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