Variant report

Variant	rs669676
Chromosome Location	chr3:99448852-99448853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10935917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1708167	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1711554	0.92[CEU][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1711564	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1718235	0.83[ASW][hapmap];0.82[LWK][hapmap];0.85[YRI][hapmap]
rs497868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498411	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs704571	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs704572	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs704574	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs704577	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7629046	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs792831	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs792833	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs792835	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs792836	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs792837	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793439	0.83[ASW][hapmap]
rs793481	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793482	0.84[ASW][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs793483	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793484	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793485	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793486	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793502	0.83[ASW][hapmap];0.82[LWK][hapmap];0.85[YRI][hapmap]
rs813218	0.83[ASW][hapmap];0.82[LWK][hapmap];0.85[YRI][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	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs669676	SENP7	cis	parietal	SCAN
rs669676	KLKB1	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99433600-99449200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:99440200-99458000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:99440400-99450200	Weak transcription	HSMMtube	muscle
4	chr3:99440400-99458000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:99440400-99458200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:99440400-99471000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:99440600-99449200	Weak transcription	NHDF-Ad	bronchial
8	chr3:99440800-99449400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:99441200-99458000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:99441400-99466800	Weak transcription	NH-A	brain
11	chr3:99443400-99471400	Weak transcription	Aorta	Aorta
12	chr3:99443800-99449800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:99448000-99451000	Strong transcription	Osteobl	bone
14	chr3:99448600-99449400	Strong transcription	HSMM	muscle
15	chr3:99448600-99450600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:99448800-99449600	Strong transcription	HUVEC	blood vessel

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