Variant report

Variant	rs7553711
Chromosome Location	chr1:173131908-173131909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10157163	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912553	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10912554	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912555	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912556	1.00[JPT][hapmap]
rs10912564	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs11811788	0.84[ASN][1000 genomes]
rs11811856	0.81[CEU][hapmap]
rs16845543	0.82[JPT][hapmap]
rs16845585	0.82[JPT][hapmap]
rs3861950	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4081545	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4090391	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916311	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916312	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916313	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56028318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661173	0.82[JPT][hapmap]
rs6665456	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691738	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514229	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7518045	0.82[JPT][hapmap]
rs7518129	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7521390	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525284	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533953	chr1:172939335-173133255	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7553711	PPP1R2	trans	cerebellum	SCAN
rs7553711	TNFSF18	cis	parietal	SCAN
rs7553711	TNN	cis	parietal	SCAN
rs7553711	FMO1	cis	cerebellum	SCAN
rs7553711	TNFSF18	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173123000-173141200	Weak transcription	HSMMtube	muscle
2	chr1:173129800-173132000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:173130200-173132200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:173130200-173132200	Enhancers	HUVEC	blood vessel
5	chr1:173130200-173132200	Enhancers	NHEK	skin
6	chr1:173130400-173132200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:173130400-173132200	Enhancers	HMEC	breast
8	chr1:173130600-173132000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:173131400-173140800	Weak transcription	HSMM	muscle
10	chr1:173131800-173132000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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