Variant report

Variant	rs918229
Chromosome Location	chr2:186574960-186574961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10174315	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180772	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10186909	0.86[EUR][1000 genomes]
rs10189129	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10190576	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209067	0.85[EUR][1000 genomes]
rs10490389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075257	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675259	0.82[EUR][1000 genomes]
rs11682752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684181	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11686377	0.81[EUR][1000 genomes]
rs11686533	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11694100	0.85[EUR][1000 genomes]
rs11891430	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11891748	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11904219	1.00[ASN][1000 genomes]
rs12328928	0.83[EUR][1000 genomes]
rs12328996	0.86[EUR][1000 genomes]
rs13410805	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13421326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421575	0.85[EUR][1000 genomes]
rs17813140	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17815052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28508191	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35119381	0.86[EUR][1000 genomes]
rs35379699	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35939893	1.00[ASN][1000 genomes]
rs56266442	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59153366	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6713671	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6716541	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749407	0.86[EUR][1000 genomes]
rs6752510	1.00[ASN][1000 genomes]
rs6753178	0.86[EUR][1000 genomes]
rs6755533	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6761099	0.86[EUR][1000 genomes]
rs72894199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896010	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72896480	0.81[EUR][1000 genomes]
rs7593451	0.85[EUR][1000 genomes]
rs7606908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875540	chr2:186345148-186583961	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875541	chr2:186345148-186598526	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv584018	chr2:186352959-186598526	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1007052	chr2:186441382-186864390	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv584019	chr2:186445393-186866874	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009118	chr2:186450293-186864390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv2763034	chr2:186473461-186587890	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1008230	chr2:186474069-186818718	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536076	chr2:186474069-186818718	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv584020	chr2:186475590-186661567	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv584021	chr2:186475590-186866841	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1011628	chr2:186523096-186594343	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1003484	chr2:186524793-186591557	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1003603	chr2:186524793-186594343	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv2751838	chr2:186531835-186591557	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv584022	chr2:186531835-186591557	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv1010456	chr2:186531835-186594343	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	esv3414312	chr2:186564235-186579049	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs918229	FSIP2	cis	parietal	SCAN
rs918229	FSIP2	cis	cerebellum	SCAN
rs918229	NCKAP1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186565600-186603200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:186574800-186575800	Weak transcription	Brain Germinal Matrix	brain

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