Variant report

Variant	rs2013064
Chromosome Location	chr12:1998044-1998045
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	MAFK	chr12:1998004-1998662	GM12878	blood:	n/a	chr12:1998283-1998298
2	SETDB1	chr12:1997622-1998064	U2OS	brain:	n/a	n/a
3	KAP1	chr12:1997712-1998085	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1976877..1978383-chr12:1995618..1998420,2	MCF-7	breast:
2	chr12:1994373..1995913-chr12:1997731..2000184,2	K562	blood:

Variant related genes	Relation type
CACNA2D4	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10735005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062005	1.00[ASW][hapmap]
rs11062007	1.00[ASW][hapmap]
rs11062008	1.00[CHB][hapmap]
rs11062010	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368779	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1558141	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1558142	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694584	1.00[ASW][hapmap]
rs17801032	1.00[CHB][hapmap]
rs1990232	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008352	1.00[ASN][1000 genomes]
rs2190769	0.84[GIH][hapmap]
rs2429155	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2429158	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429163	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429164	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429167	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2429168	1.00[ASN][1000 genomes]
rs2429169	1.00[CHB][hapmap]
rs2429184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470409	1.00[ASN][1000 genomes]
rs2470428	0.86[CEU][hapmap]
rs2470438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470439	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2906892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906893	0.84[GIH][hapmap]
rs720456	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304762	0.91[CEU][hapmap]
rs7315910	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap]
rs758157	1.00[ASN][1000 genomes]
rs758158	1.00[CHB][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs7961753	1.00[ASW][hapmap]
rs7967890	1.00[ASW][hapmap]
rs8181666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181681	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886939	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs886941	1.00[CHB][hapmap];0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1046388	chr12:1964846-2034887	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1043329	chr12:1986238-2034887	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv518786	chr12:1998044-2016322	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1997400-1999400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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