Variant report

Variant	rs17604831
Chromosome Location	chr2:31664302-31664303
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1033688	0.97[ASN][1000 genomes]
rs1033689	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1033690	0.97[ASN][1000 genomes]
rs11124260	0.96[ASN][1000 genomes]
rs11124261	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11526116	0.95[ASN][1000 genomes]
rs11526117	0.95[ASN][1000 genomes]
rs11674100	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11679875	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467131	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12468955	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469125	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12473298	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12479415	0.90[ASN][1000 genomes]
rs1429372	0.90[CHB][hapmap]
rs17545406	0.94[ASN][1000 genomes]
rs17545483	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17604588	0.93[ASN][1000 genomes]
rs1884723	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978638	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1978639	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs206808	0.80[EUR][1000 genomes]
rs206811	0.81[CHD][hapmap]
rs206812	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2073316	0.80[CHB][hapmap]
rs2163058	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365772	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2365778	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28810790	0.82[ASN][1000 genomes]
rs28815209	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28879135	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34096339	0.91[ASN][1000 genomes]
rs4622775	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4952215	0.91[ASN][1000 genomes]
rs4952236	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952251	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4952263	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55933129	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56247470	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56271553	0.91[ASN][1000 genomes]
rs58071748	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58364223	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58967340	0.96[ASN][1000 genomes]
rs59770035	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59964343	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60441502	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60989770	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61316601	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61706447	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62141223	0.90[ASN][1000 genomes]
rs66492775	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710918	0.87[ASN][1000 genomes]
rs67603251	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67830899	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790682	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72794621	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7575607	0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7585845	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595578	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7602067	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766273	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9636426	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv999815	chr2:31654667-31777296	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17604831	IFT172	cis	parietal	SCAN
rs17604831	SLC30A6	cis	cerebellum	SCAN
rs17604831	NLRC4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31653400-31669600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:31662800-31664400	Enhancers	Osteobl	bone
3	chr2:31662800-31665400	Enhancers	NHDF-Ad	bronchial
4	chr2:31663000-31664400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:31663000-31664400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:31663000-31665600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:31663200-31664400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:31663200-31664600	Enhancers	HSMM	muscle
9	chr2:31663200-31664600	Enhancers	NHEK	skin
10	chr2:31663400-31664400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:31663800-31664400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:31663800-31664400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:31663800-31664400	Enhancers	HMEC	breast
14	chr2:31663800-31664400	Enhancers	HSMMtube	muscle
15	chr2:31663800-31664600	Enhancers	NHLF	lung
16	chr2:31664200-31669400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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