Variant report

Variant	rs4628468
Chromosome Location	chr1:179604864-179604865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:179604467-179604892	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:179604481-179604880	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:179604416-179604889	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:179604455-179604909	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179601476..179603491-chr1:179604853..179608456,3	MCF-7	breast:

Variant related genes	Relation type
TDRD5	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10157699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798704	0.95[YRI][hapmap]
rs10798708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs10913847	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs11582158	0.89[CEU][hapmap]
rs12724901	0.89[CEU][hapmap]
rs12747675	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12751914	1.00[CEU][hapmap]
rs12758828	0.89[CEU][hapmap]
rs1328595	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs1410594	0.86[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1590783	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35229401	0.91[EUR][1000 genomes]
rs35448215	0.94[EUR][1000 genomes]
rs3930537	1.00[CHB][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs4443850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4651043	0.81[CEU][hapmap]
rs4651044	0.81[LWK][hapmap];0.96[YRI][hapmap]
rs4652418	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4652420	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs4652421	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs4652428	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs4652430	1.00[CEU][hapmap]
rs7534216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7549258	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013000	chr1:179589193-179628536	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4628468	EIF3E	trans	cerebellum	SCAN
rs4628468	NPHS2	cis	cerebellum	SCAN
rs4628468	TDRD5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179604200-179607200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:179604800-179605000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links