Variant report

Variant	rs4928040
Chromosome Location	chr3:54356753-54356754
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	chr1:91852589..91853107-chr3:54356271..54356793,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11130416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445645	0.95[EUR][1000 genomes]
rs6445648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6810202	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427630	0.94[EUR][1000 genomes]
rs7429094	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]
rs7431577	1.00[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.95[EUR][1000 genomes]
rs7434239	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618315	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627905	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7632823	0.84[TSI][hapmap]
rs7634811	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7652209	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9683195	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9818348	0.91[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9849660	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9863855	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs9879885	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS 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	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4928040	TEX264	cis	parietal	SCAN
rs4928040	CCDC66	cis	parietal	SCAN
rs4928040	TUSC2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54344000-54360800	Weak transcription	Psoas Muscle	Psoas
2	chr3:54352800-54357600	Enhancers	Hela-S3	cervix
3	chr3:54354600-54356800	Enhancers	Placenta	Placenta
4	chr3:54354600-54357400	Enhancers	Liver	Liver
5	chr3:54355400-54357200	Enhancers	Fetal Intestine Large	intestine
6	chr3:54355400-54357200	Enhancers	Fetal Intestine Small	intestine
7	chr3:54355600-54357200	Enhancers	Fetal Kidney	kidney
8	chr3:54355600-54357200	Enhancers	Fetal Lung	lung
9	chr3:54355800-54356800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:54355800-54357200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:54355800-54357400	Enhancers	Stomach Mucosa	stomach
12	chr3:54356000-54356800	Enhancers	Fetal Brain Male	brain
13	chr3:54356000-54357200	Enhancers	Colonic Mucosa	Colon
14	chr3:54356000-54357200	Enhancers	HepG2	liver
15	chr3:54356000-54357400	Enhancers	Gastric	stomach
16	chr3:54356000-54357400	Enhancers	Pancreas	Pancrea
17	chr3:54356600-54357000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:54356600-54357000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:54356600-54370200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links