Variant report

Variant	rs1422997
Chromosome Location	chr5:147393664-147393665
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10058108	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062911	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064815	0.83[EUR][1000 genomes]
rs10067434	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069070	0.81[CEU][hapmap]
rs1017222	0.81[CEU][hapmap]
rs10463395	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10463396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12108690	0.81[CEU][hapmap]
rs1363727	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363728	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363729	0.81[CEU][hapmap]
rs1422982	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1422998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423000	0.81[CEU][hapmap]
rs1423001	0.81[CEU][hapmap]
rs1423003	0.81[CEU][hapmap]
rs1423004	0.81[CEU][hapmap]
rs1423007	0.81[CEU][hapmap]
rs17626088	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052529	0.83[EUR][1000 genomes]
rs2216655	0.83[EUR][1000 genomes]
rs2287772	0.88[CEU][hapmap]
rs28576989	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895729	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs3752676	0.81[CEU][hapmap]
rs3756688	0.81[CEU][hapmap]
rs4357026	0.81[CEU][hapmap]
rs4415068	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4472254	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap]
rs4529181	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap]
rs4705218	0.82[EUR][1000 genomes]
rs6580519	0.84[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap]
rs6580520	0.84[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap]
rs6864564	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap]
rs6864920	0.84[CEU][hapmap]
rs6891643	0.81[EUR][1000 genomes]
rs6895394	0.83[EUR][1000 genomes]
rs7701882	0.80[EUR][1000 genomes]
rs7704424	0.81[EUR][1000 genomes]
rs7713918	0.81[EUR][1000 genomes]
rs7716414	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325061	0.81[CEU][hapmap]
rs9325064	0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1422997	SPINK5	cis	Heart Left Ventricle	GTEx
rs1422997	SPINK5	cis	Thyroid	GTEx
rs1422997	ZNF300P1	cis	parietal	SCAN
rs1422997	SPINK5	cis	Muscle Skeletal	GTEx
rs1422997	ADRB2	cis	parietal	SCAN
rs1422997	SPINK5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147386400-147394000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:147386400-147400000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:147388600-147401800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:147389200-147394400	Enhancers	Hela-S3	cervix
5	chr5:147390600-147394600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:147391000-147394400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:147391000-147394400	Enhancers	HMEC	breast
8	chr5:147391000-147394400	Enhancers	NHEK	skin
9	chr5:147391600-147400800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:147391800-147401600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:147392600-147396200	Weak transcription	Psoas Muscle	Psoas
12	chr5:147393200-147394200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:147393400-147393800	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links