Variant report

Variant	rs12363545
Chromosome Location	chr11:5777096-5777097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1032647	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1032648	0.97[ASN][1000 genomes]
rs1032649	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs11038925	0.94[CHB][hapmap]
rs11038928	0.93[CHB][hapmap]
rs11038937	0.93[CHB][hapmap]
rs11038940	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs11038942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11038944	0.88[CHB][hapmap]
rs11038945	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs11038946	0.94[CHB][hapmap]
rs11038949	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap]
rs11038952	0.88[CHB][hapmap]
rs11038961	0.94[CHB][hapmap]
rs11038962	0.94[CHB][hapmap]
rs11038963	1.00[CHB][hapmap]
rs11038979	0.93[CHB][hapmap]
rs11039025	0.94[CHB][hapmap]
rs11039038	0.88[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs11039053	0.94[CHB][hapmap]
rs11039100	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11039101	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs11039110	0.82[ASN][1000 genomes]
rs11039115	0.82[ASN][1000 genomes]
rs11039116	0.82[ASN][1000 genomes]
rs11039117	0.82[ASN][1000 genomes]
rs11039118	0.82[ASN][1000 genomes]
rs11039120	0.82[ASN][1000 genomes]
rs11039121	0.82[ASN][1000 genomes]
rs11039164	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs11039168	0.93[JPT][hapmap]
rs11039170	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs11826964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11828490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12361754	0.89[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs12362071	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12362742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12362750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12362906	0.94[CHB][hapmap]
rs12363178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12363725	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs12363853	0.82[ASN][1000 genomes]
rs12363855	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12364119	0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12364223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12364265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12364563	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12364723	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12364796	0.87[MEX][hapmap]
rs12365487	0.94[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap]
rs12365564	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12365568	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12366070	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12791839	0.82[ASN][1000 genomes]
rs12792672	0.81[ASN][1000 genomes]
rs12792905	0.82[ASN][1000 genomes]
rs12792952	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12793142	0.80[ASN][1000 genomes]
rs12793267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12794769	0.94[CHB][hapmap]
rs12796660	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs12797407	0.83[CHB][hapmap]
rs12798822	0.82[ASN][1000 genomes]
rs12798823	0.82[ASN][1000 genomes]
rs1470872	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs1470873	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1498557	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498558	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2047460	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2047461	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2047462	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2880343	0.94[CHB][hapmap]
rs34037040	0.83[ASN][1000 genomes]
rs34123108	0.83[ASN][1000 genomes]
rs34161300	0.82[ASN][1000 genomes]
rs34286221	0.83[ASN][1000 genomes]
rs34317277	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34818213	0.83[ASN][1000 genomes]
rs34930440	0.82[ASN][1000 genomes]
rs35466594	0.82[ASN][1000 genomes]
rs35746872	0.82[ASN][1000 genomes]
rs35863959	0.83[ASN][1000 genomes]
rs35863965	0.82[ASN][1000 genomes]
rs35916605	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35990969	0.82[ASN][1000 genomes]
rs4280027	0.82[ASN][1000 genomes]
rs4319539	0.82[ASN][1000 genomes]
rs4414254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4474469	0.82[ASN][1000 genomes]
rs4561239	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4597095	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4636704	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4636705	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5012841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5012842	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5012843	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61875860	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61875861	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61875862	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61875914	0.82[ASN][1000 genomes]
rs61875915	0.82[ASN][1000 genomes]
rs72896130	0.83[ASN][1000 genomes]
rs7395852	0.93[GIH][hapmap]
rs968991	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968992	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv553277	chr11:5722948-6010075	Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	esv1843296	chr11:5730377-5970717	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv2758255	chr11:5730377-5970717	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	esv2759801	chr11:5730377-6007613	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv896950	chr11:5740634-5827540	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
14	nsv832058	chr11:5747594-5926814	Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
15	esv1817137	chr11:5759141-5809172	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	esv1805431	chr11:5760056-5809358	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
17	esv1820513	chr11:5760106-5809230	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	nsv553288	chr11:5760106-5809811	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
19	nsv553292	chr11:5760172-5809230	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
20	nsv553295	chr11:5760947-5805515	Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
21	esv33342	chr11:5770370-5784484	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv1055011	chr11:5770388-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
23	nsv896951	chr11:5773981-5832191	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
24	nsv553306	chr11:5775730-5805515	Inactive region	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
25	nsv1035915	chr11:5776528-5809127	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
26	nsv1050906	chr11:5776528-5809449	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
27	esv1823465	chr11:5776595-5809230	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
28	nsv553307	chr11:5776595-5809230	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
29	esv2757421	chr11:5776623-5842356	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
30	nsv1044755	chr11:5776980-5809449	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
31	esv1826181	chr11:5777023-5809477	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
32	esv1798649	chr11:5777096-5808353	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
33	esv1801544	chr11:5777096-5808353	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
34	esv1822319	chr11:5777096-5808353	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
35	esv1823568	chr11:5777096-5808353	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12363545	LSP1	cis	parietal	SCAN
rs12363545	MRPL17	cis	cerebellum	SCAN
rs12363545	UBQLN3	cis	cerebellum	SCAN
rs12363545	HBB	cis	cerebellum	SCAN
rs12363545	ASCL2	cis	cerebellum	SCAN
rs12363545	OR5P2	cis	cerebellum	SCAN
rs12363545	ILK	cis	cerebellum	SCAN
rs12363545	OR51F1	cis	parietal	SCAN
rs12363545	NRIP3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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