Variant report

Variant	rs7713918
Chromosome Location	chr5:147413651-147413652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10058108	0.80[EUR][1000 genomes]
rs10064815	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10067434	0.81[EUR][1000 genomes]
rs10069070	0.84[CEU][hapmap]
rs10073775	0.80[CEU][hapmap]
rs1007978	0.80[CEU][hapmap]
rs1017222	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs10463396	0.83[EUR][1000 genomes]
rs12108690	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs12519144	0.80[CEU][hapmap]
rs1363727	0.81[EUR][1000 genomes]
rs1363728	0.81[EUR][1000 genomes]
rs1363729	0.84[CEU][hapmap]
rs1422982	0.84[EUR][1000 genomes]
rs1422992	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1422993	0.91[CHD][hapmap]
rs1422997	0.81[EUR][1000 genomes]
rs1422998	0.81[EUR][1000 genomes]
rs1423000	0.84[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap]
rs1423001	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs1423002	0.80[CEU][hapmap]
rs1423003	0.84[CEU][hapmap]
rs1423004	0.84[CEU][hapmap]
rs1423006	0.80[CEU][hapmap]
rs1423007	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs1423008	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1609851	0.84[CEU][hapmap]
rs1862439	0.82[CHD][hapmap];0.84[GIH][hapmap]
rs1862446	0.82[CHD][hapmap]
rs2052529	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2216655	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2895729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752676	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs3756688	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs3822744	0.80[CEU][hapmap]
rs4357026	0.84[CEU][hapmap]
rs4705218	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580519	0.81[CEU][hapmap]
rs6580520	0.81[CEU][hapmap]
rs6864920	0.81[CEU][hapmap]
rs6891643	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6895394	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7701882	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7704424	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7716414	0.82[EUR][1000 genomes]
rs9325061	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs9325064	0.84[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs9325073	0.91[CHD][hapmap]
rs986494	0.91[CHD][hapmap]
rs988885	0.84[GIH][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	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1033838	chr5:147360521-147484014	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv933016	chr5:147395849-147453701	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv933225	chr5:147395849-147486560	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7713918	SPINK5	cis	Thyroid	GTEx
rs7713918	ZNF300P1	cis	parietal	SCAN
rs7713918	NHP2L1	trans	parietal	SCAN
rs7713918	GABPB2	trans	parietal	SCAN
rs7713918	SPINK5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147411600-147414200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:147411600-147414400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:147412400-147413800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:147412400-147414200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr5:147412600-147414000	Enhancers	Hela-S3	cervix
6	chr5:147412800-147418000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:147413200-147413800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:147413400-147413800	Enhancers	Placenta	Placenta
9	chr5:147413600-147434200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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