Variant report

Variant	rs12534480
Chromosome Location	chr7:78613510-78613511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1006818	0.89[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs10215372	0.88[EUR][1000 genomes]
rs10224972	0.82[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap]
rs10231279	0.85[CHD][hapmap]
rs10236354	0.88[EUR][1000 genomes]
rs10240536	0.83[CHB][hapmap]
rs10259881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs10269689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10485926	0.83[CHB][hapmap]
rs1073416	0.90[CEU][hapmap];0.93[TSI][hapmap]
rs10808175	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12113491	0.84[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs12536843	0.88[EUR][1000 genomes]
rs12537793	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12538053	0.88[EUR][1000 genomes]
rs12669763	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12705911	0.88[EUR][1000 genomes]
rs13438061	0.83[CHB][hapmap]
rs13438576	0.83[CHB][hapmap]
rs1476106	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2006635	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2078428	0.90[CEU][hapmap]
rs2109713	0.89[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2191724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2215546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap]
rs2215547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2280608	0.88[EUR][1000 genomes]
rs34086589	0.88[EUR][1000 genomes]
rs4730596	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4730599	0.89[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs4730601	0.89[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs6466468	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466471	0.86[EUR][1000 genomes]
rs727652	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs763593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7779315	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7781812	0.87[EUR][1000 genomes]
rs7789063	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7793390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797398	0.88[EUR][1000 genomes]
rs7799032	0.88[EUR][1000 genomes]
rs7805367	0.89[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs7807319	0.87[EUR][1000 genomes]
rs7809089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9656215	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9692247	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv482826	chr7:78548319-78717605	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471642	chr7:78548320-78717605	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12534480	SRCRB4D	cis	cerebellum	SCAN
rs12534480	MDH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78613400-78613800	Weak transcription	Aorta	Aorta

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