Variant report

Variant	rs4985969
Chromosome Location	chr17:20949688-20949689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20948417..20950134-chr17:20958471..20960661,2	MCF-7	breast:
2	chr17:20944792..20946565-chr17:20947999..20949921,2	K562	blood:
3	chr17:20944841..20947383-chr17:20948127..20950717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1045162	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1127814	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11867648	0.89[MKK][hapmap]
rs12051606	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12600703	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12601292	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12602058	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12943067	0.87[ASN][1000 genomes]
rs12946114	0.87[ASN][1000 genomes]
rs1542552	0.87[CHD][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17770614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054464	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2127095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291034	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2364326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2886105	0.86[AMR][1000 genomes]
rs4445951	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985811	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985814	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985815	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985816	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985959	0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4985963	0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4985966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985967	0.86[ASN][1000 genomes]
rs4985968	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985970	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985971	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985975	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56323013	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58235085	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59543297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59713572	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587111	0.82[ASN][1000 genomes]
rs6587114	0.87[ASN][1000 genomes]
rs6618	0.84[ASN][1000 genomes]
rs719093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7209129	0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7216921	0.82[ASN][1000 genomes]
rs880653	0.86[AMR][1000 genomes]
rs899337	0.87[AMR][1000 genomes]
rs899340	0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9911289	0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][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	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv827918	chr17:20941127-20951156	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv827921	chr17:20943553-20951115	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4985969	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs4985969	RP11-344E13.3	cis	lung	GTEx
rs4985969	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs4985969	RP11-344E13.3	cis	Whole Blood	GTEx
rs4985969	RP11-344E13.3	cis	Thyroid	GTEx
rs4985969	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4985969	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs4985969	RP11-344E13.3	cis	Stomach	GTEx
rs4985969	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs4985969	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs4985969	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs4985969	RP11-344E13.3	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20947800-20955000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr17:20947800-20955000	Weak transcription	Fetal Lung	lung
3	chr17:20947800-20955200	Weak transcription	Pancreas	Pancrea

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