Variant report

Variant	rs11587012
Chromosome Location	chr1:152759204-152759205
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10157301	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048535	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494277	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788847	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10888514	0.82[CEU][hapmap]
rs11205086	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11578927	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581045	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11582063	0.89[ASN][1000 genomes]
rs11585409	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11586156	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587180	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094874	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239774	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725760	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728274	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12733893	1.00[JPT][hapmap]
rs12747888	0.89[ASN][1000 genomes]
rs12754243	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12754873	1.00[JPT][hapmap]
rs1412541	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1412548	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1591077	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs17624493	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17661905	0.89[ASN][1000 genomes]
rs1888964	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1930127	0.87[CEU][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap]
rs2339381	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879458	0.91[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34384421	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35274012	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35393920	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36012879	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41268484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353097	0.89[ASN][1000 genomes]
rs4539140	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845473	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4845474	1.00[ASN][1000 genomes]
rs4845482	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683499	0.89[ASN][1000 genomes]
rs56130300	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180022	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812714	1.00[ASN][1000 genomes]
rs6587706	0.91[EUR][1000 genomes]
rs7524281	0.91[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs7539924	0.89[ASN][1000 genomes]
rs7550666	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:62 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv33483	chr1:152550269-152775526	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv547891	chr1:152556085-152770446	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv947325	chr1:152670204-152793272	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
12	esv2763813	chr1:152687058-152780522	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv508615	chr1:152724155-152787503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv1004884	chr1:152724514-152780522	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv1005867	chr1:152744949-152768688	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv1010895	chr1:152744949-152776743	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv79	chr1:152746435-152773598	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv2910	chr1:152746435-152774414	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
19	nsv1014190	chr1:152747126-152778861	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1001012	chr1:152749733-152763057	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1004508	chr1:152749733-152768688	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv997705	chr1:152749733-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv998888	chr1:152749733-152776743	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv1001721	chr1:152750256-152768688	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv1009988	chr1:152750256-152773905	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv1003849	chr1:152750506-152768688	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	nsv1001837	chr1:152750506-152773905	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
29	nsv1009915	chr1:152750658-152768688	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv1010924	chr1:152750658-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	nsv1011430	chr1:152750710-152773905	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
32	nsv1002796	chr1:152751225-152763057	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv1000650	chr1:152751225-152768688	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
34	nsv1009758	chr1:152751225-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
35	esv1813620	chr1:152751946-152774632	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
36	esv1799962	chr1:152751946-152778711	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
37	esv1836202	chr1:152754630-152763057	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
38	nsv1011877	chr1:152754630-152767741	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
39	nsv1001998	chr1:152754630-152767951	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
40	nsv1003430	chr1:152754630-152768688	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
41	nsv1007168	chr1:152754630-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
42	esv3501633	chr1:152754928-152772360	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
43	esv3501634	chr1:152754928-152772360	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
44	nsv1004337	chr1:152756296-152768688	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
45	nsv1001922	chr1:152756774-152768347	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
46	nsv998434	chr1:152757690-152767741	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
47	nsv1013364	chr1:152757690-152767852	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
48	nsv1009870	chr1:152757690-152767951	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
49	nsv1011806	chr1:152757690-152768247	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
50	nsv999851	chr1:152757690-152768688	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11587012	SMCP	cis	cerebellum	SCAN
rs11587012	LCE1D	cis	Skin Sun Exposed Lower leg	GTEx
rs11587012	S100A14	cis	cerebellum	SCAN
rs11587012	LCE1E	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152758400-152759400	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr1:152758400-152759400	Flanking Active TSS	HMEC	breast
3	chr1:152759000-152759400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:152759000-152759400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:152759200-152759800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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