Variant report

Variant	rs2216655
Chromosome Location	chr5:147394348-147394349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10064815	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067434	0.82[EUR][1000 genomes]
rs10069070	0.85[CEU][hapmap]
rs10073775	0.81[CEU][hapmap]
rs1007978	0.81[CEU][hapmap]
rs1017222	0.84[CEU][hapmap]
rs10463395	0.81[EUR][1000 genomes]
rs10463396	0.81[EUR][1000 genomes]
rs12108690	0.84[CEU][hapmap]
rs12519144	0.81[CEU][hapmap]
rs1363727	0.84[EUR][1000 genomes]
rs1363728	0.84[EUR][1000 genomes]
rs1363729	0.85[CEU][hapmap]
rs1422982	0.81[EUR][1000 genomes]
rs1422992	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1422997	0.83[EUR][1000 genomes]
rs1422998	0.83[EUR][1000 genomes]
rs1423000	0.84[CEU][hapmap]
rs1423001	0.84[CEU][hapmap]
rs1423002	0.81[CEU][hapmap]
rs1423003	0.85[CEU][hapmap]
rs1423004	0.85[CEU][hapmap]
rs1423006	0.81[CEU][hapmap]
rs1423007	0.84[CEU][hapmap]
rs1423008	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1609851	0.84[CEU][hapmap]
rs2052529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752676	0.84[CEU][hapmap]
rs3756688	0.84[CEU][hapmap]
rs3822744	0.81[CEU][hapmap]
rs4357026	0.85[CEU][hapmap]
rs4519912	0.81[CEU][hapmap]
rs4705218	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580519	0.81[CEU][hapmap]
rs6580520	0.81[CEU][hapmap]
rs6891643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701882	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713918	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7716414	0.81[EUR][1000 genomes]
rs9325061	0.84[CEU][hapmap]
rs9325064	0.84[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2216655	SPINK5	cis	Thyroid	GTEx
rs2216655	SPINK5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:11 , 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	chr5:147389200-147394400	Enhancers	Hela-S3	cervix
4	chr5:147390600-147394600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:147391000-147394400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:147391000-147394400	Enhancers	HMEC	breast
7	chr5:147391000-147394400	Enhancers	NHEK	skin
8	chr5:147391600-147400800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:147391800-147401600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:147392600-147396200	Weak transcription	Psoas Muscle	Psoas
11	chr5:147394000-147394600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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