Variant report

Variant	rs7727177
Chromosome Location	chr5:147413756-147413757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10058108	0.84[AFR][1000 genomes]
rs10062911	0.84[AFR][1000 genomes]
rs10067434	0.89[AFR][1000 genomes]
rs10463396	0.93[AFR][1000 genomes]
rs10477360	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12514503	0.81[ASN][1000 genomes]
rs1422982	0.91[AFR][1000 genomes]
rs1422992	0.91[AFR][1000 genomes]
rs1549237	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28576989	0.84[AFR][1000 genomes]
rs4415068	0.89[AFR][1000 genomes]
rs7716414	0.92[AFR][1000 genomes]
rs9325065	0.81[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7727177	SPINK5	cis	Thyroid	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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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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