Variant report

Variant	rs1423008
Chromosome Location	chr5:147429494-147429495
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10058108	0.84[EUR][1000 genomes]
rs10062911	0.83[EUR][1000 genomes]
rs10064815	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10069070	1.00[YRI][hapmap]
rs10073775	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10463396	0.80[EUR][1000 genomes]
rs11745768	1.00[YRI][hapmap]
rs12108690	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12521759	0.81[AFR][1000 genomes]
rs1363729	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1422982	0.81[EUR][1000 genomes]
rs1423000	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1423001	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1423003	1.00[YRI][hapmap]
rs1833768	0.81[AFR][1000 genomes]
rs1862439	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1862445	1.00[YRI][hapmap]
rs1862446	1.00[YRI][hapmap]
rs2052529	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2216655	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28576989	0.82[EUR][1000 genomes]
rs2895729	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756688	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3777140	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3777143	1.00[YRI][hapmap]
rs3815737	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3822744	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4357026	1.00[YRI][hapmap]
rs4519912	0.81[AFR][1000 genomes]
rs4705218	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705223	1.00[YRI][hapmap]
rs6891643	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895394	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7701882	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7704424	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713918	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1423008	SPINK5	cis	Heart Left Ventricle	GTEx
rs1423008	SPINK5	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147413600-147434200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:147426600-147433400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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