Variant report

Variant	rs1363727
Chromosome Location	chr5:147394450-147394451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10058108	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062911	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064815	0.84[EUR][1000 genomes]
rs10067434	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463395	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10463396	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363728	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422982	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422992	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422997	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17626088	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052529	0.83[EUR][1000 genomes]
rs2216655	0.84[EUR][1000 genomes]
rs28576989	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895729	0.84[EUR][1000 genomes]
rs4415068	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4705218	0.82[EUR][1000 genomes]
rs6891643	0.81[EUR][1000 genomes]
rs6895394	0.83[EUR][1000 genomes]
rs7704424	0.81[EUR][1000 genomes]
rs7713918	0.81[EUR][1000 genomes]
rs7716414	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1363727	SPINK5	cis	Thyroid	GTEx
rs1363727	SPINK5	cis	Adipose Subcutaneous	GTEx
rs1363727	SPINK5	cis	Heart Left Ventricle	GTEx
rs1363727	SPINK5	cis	Muscle Skeletal	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147386400-147400000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:147388600-147401800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:147390600-147394600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:147391600-147400800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:147391800-147401600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:147392600-147396200	Weak transcription	Psoas Muscle	Psoas
7	chr5:147394000-147394600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:147394400-147398600	Weak transcription	Hela-S3	cervix

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