Variant report

Variant	rs1422992
Chromosome Location	chr5:147405107-147405108
allele	C/T
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	GATA3	chr5:147404811-147405190	MCF-7	breast:	n/a	chr5:147405048-147405057
2	GATA2	chr5:147404859-147405150	HUVEC	blood vessel:	n/a	chr5:147405048-147405057

Variant related genes	Relation type
SPINK5	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10058108	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062911	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064815	0.82[EUR][1000 genomes]
rs10067434	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069070	0.82[CEU][hapmap]
rs1017222	0.81[CEU][hapmap]
rs10463395	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10463396	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477360	0.94[AFR][1000 genomes]
rs12108690	0.81[CEU][hapmap]
rs1363727	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363728	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363729	0.82[CEU][hapmap]
rs1422982	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422997	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422998	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423000	0.81[CEU][hapmap]
rs1423001	0.81[CEU][hapmap]
rs1423003	0.82[CEU][hapmap]
rs1423004	0.82[CEU][hapmap]
rs1423007	0.81[CEU][hapmap]
rs1549237	0.94[AFR][1000 genomes]
rs1609851	0.81[CEU][hapmap]
rs17626088	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052529	0.82[EUR][1000 genomes]
rs2216655	0.82[EUR][1000 genomes]
rs2287772	0.89[CEU][hapmap]
rs28576989	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895729	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs3752676	0.81[CEU][hapmap]
rs3756688	0.81[CEU][hapmap]
rs4357026	0.82[CEU][hapmap]
rs4415068	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4472254	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs4519912	0.80[CEU][hapmap]
rs4529181	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs4705218	0.84[EUR][1000 genomes]
rs6580519	0.84[CEU][hapmap]
rs6580520	0.84[CEU][hapmap]
rs6864564	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs6864920	0.85[CEU][hapmap];0.80[CHB][hapmap]
rs6891643	0.81[EUR][1000 genomes]
rs6895394	0.83[EUR][1000 genomes]
rs7701882	0.81[EUR][1000 genomes]
rs7704424	0.81[EUR][1000 genomes]
rs7713918	0.81[EUR][1000 genomes]
rs7716414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727177	0.91[AFR][1000 genomes]
rs9325061	0.81[CEU][hapmap]
rs9325064	0.81[CEU][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1422992	SPINK5	cis	Muscle Skeletal	GTEx
rs1422992	SPINK5	cis	Thyroid	GTEx
rs1422992	SPINK5	cis	Adipose Subcutaneous	GTEx
rs1422992	SPINK5	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147400600-147409800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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