Variant report

Variant	rs300951
Chromosome Location	chr4:144201383-144201384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:144105045..144106562-chr4:144200754..144203698,2	MCF-7	breast:
2	chr4:144200658..144204574-chr4:144257489..144259349,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170185	Chromatin interaction
ENSG00000250326	Chromatin interaction
ENSG00000178972	Chromatin interaction
ENSG00000109458	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10000911	0.81[CEU][hapmap]
rs10012713	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10028909	0.95[ASN][1000 genomes]
rs10033104	0.81[EUR][1000 genomes]
rs10155434	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs10434185	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs11100779	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs11947952	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12501994	0.82[CHD][hapmap]
rs12643013	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13102579	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13114280	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13118846	0.88[ASN][1000 genomes]
rs13118943	0.84[EUR][1000 genomes]
rs13129434	0.95[ASN][1000 genomes]
rs13137362	0.95[ASN][1000 genomes]
rs13137565	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs1532981	0.88[ASN][1000 genomes]
rs2119269	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs300894	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs300899	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs300901	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs300902	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs300903	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs300913	0.95[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs300914	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs300915	0.95[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs300917	0.95[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs300921	0.83[EUR][1000 genomes]
rs300924	0.84[EUR][1000 genomes]
rs300925	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs300927	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs300929	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs300938	0.81[EUR][1000 genomes]
rs300940	0.81[EUR][1000 genomes]
rs300941	0.81[EUR][1000 genomes]
rs300943	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs300946	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs300947	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs300949	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs300953	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285045	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs4413361	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs4690780	0.86[CHB][hapmap]
rs4690783	0.84[EUR][1000 genomes]
rs476417	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs592349	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs624170	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6537152	0.95[ASN][1000 genomes]
rs6537153	0.84[ASN][1000 genomes]
rs666542	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6820340	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs6823434	0.95[ASN][1000 genomes]
rs6840603	0.87[ASN][1000 genomes]
rs7435424	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs7436840	0.83[EUR][1000 genomes]
rs763918	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7655782	0.88[ASN][1000 genomes]
rs7690761	0.88[ASN][1000 genomes]
rs7692813	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs9996072	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs9998017	0.86[CEU][hapmap];0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv880177	chr4:144174773-144214082	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs300951	SLC10A7	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144197800-144202600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr4:144200400-144202000	Weak transcription	Fetal Stomach	stomach
3	chr4:144200400-144202800	Weak transcription	Adipose Nuclei	Adipose
4	chr4:144200600-144201400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:144200600-144202000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links