Variant report

Variant	rs3916566
Chromosome Location	chr1:154282146-154282147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154281131..154283820-chr1:154289105..154291104,2	K562	blood:
2	chr1:154280303..154282360-chr1:154284259..154286471,2	K562	blood:
3	chr1:154280637..154282180-chr1:154296341..154298775,2	MCF-7	breast:
4	chr1:154273544..154275651-chr1:154279583..154282150,2	K562	blood:

Variant related genes	Relation type
ENSG00000143515	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11809740	0.95[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs12729561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1352333	0.92[EUR][1000 genomes]
rs1626035	0.92[EUR][1000 genomes]
rs1760796	0.95[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs1931299	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274988	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2297606	0.83[CEU][hapmap]
rs2297607	0.87[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes]
rs2481064	0.92[EUR][1000 genomes]
rs2483710	0.92[EUR][1000 genomes]
rs2483711	0.91[EUR][1000 genomes]
rs2988721	0.95[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs34640592	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880256	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34968830	0.89[ASN][1000 genomes]
rs35362987	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35387092	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35463210	0.93[EUR][1000 genomes]
rs35800693	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811452	0.84[ASN][1000 genomes]
rs56023096	0.88[AFR][1000 genomes]
rs56367957	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61578738	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6427561	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686621	0.94[ASN][1000 genomes]
rs749966	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7547298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787014	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3916566	C1orf43	cis	parietal	SCAN
rs3916566	RORC	cis	cerebellum	SCAN
rs3916566	SCAMP3	cis	parietal	SCAN
rs3916566	S100A14	cis	cerebellum	SCAN
rs3916566	PIP5K1A	cis	cerebellum	SCAN
rs3916566	CKS1B	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154281200-154284000	Weak transcription	K562	blood
2	chr1:154282000-154293400	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links