Variant report

Variant	rs429643
Chromosome Location	chr20:14470349-14470350
allele	A/G
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	TCF12	chr20:14469883-14470684	A549	lung:	n/a	n/a
2	FOXA2	chr20:14470056-14470462	A549	lung:	n/a	chr20:14470328-14470340

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:14469605..14471318-chr20:14479870..14481906,2	MCF-7	breast:

Variant related genes	Relation type
MACROD2	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs13036305	0.89[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13036870	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13037403	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13037982	0.89[CEU][hapmap]
rs13039094	0.89[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13039304	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13040047	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13041600	0.82[TSI][hapmap]
rs13042875	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13043292	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13043921	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs17227062	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17812701	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17812707	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17812713	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17812749	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1815494	0.89[YRI][hapmap]
rs1998103	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1998104	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2327859	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2423789	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2423795	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2423796	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2423797	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2423798	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2423799	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2423801	0.84[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34202312	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34366310	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35658161	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36023726	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs365225	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs365792	1.00[YRI][hapmap]
rs366944	0.91[YRI][hapmap]
rs373874	0.93[CEU][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs376577	0.89[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs376972	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs377610	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs384498	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs391092	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs398372	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs405620	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs405993	0.81[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs406307	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs406441	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs407908	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs408176	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs412345	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41328645	0.82[TSI][hapmap]
rs416436	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs420299	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs420629	1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs429495	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs430452	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs436322	0.94[CEU][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs441540	0.89[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs441647	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs453013	0.88[MKK][hapmap]
rs4630827	0.82[TSI][hapmap]
rs475471	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4814304	0.92[YRI][hapmap]
rs4814307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6042732	0.92[YRI][hapmap]
rs6079442	0.92[YRI][hapmap]
rs6079476	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6110316	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62202873	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs915076	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1064721	chr20:14384931-14648223	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv833926	chr20:14410153-14572336	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv585442	chr20:14420556-14485947	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1065426	chr20:14426642-14478256	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1059770	chr20:14432394-14549781	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv544187	chr20:14432394-14549781	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv529577	chr20:14434373-14799157	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs429643	L1TD1	trans	lymphoblastoid	seeQTL
rs429643	FLRT3	cis	parietal	SCAN
rs429643	PCSK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14460800-14477600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:14462600-14488400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:14469200-14471400	Enhancers	HUVEC	blood vessel
4	chr20:14470000-14471200	Weak transcription	Stomach Mucosa	stomach
5	chr20:14470200-14471000	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links