Variant report

Variant	rs10742787
Chromosome Location	chr11:5809746-5809747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10047437	0.97[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs10734554	0.87[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs10742788	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]
rs10742789	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10742793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10742796	0.93[ASN][1000 genomes]
rs10769224	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10769232	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]
rs10769235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769240	0.87[EUR][1000 genomes]
rs10769241	0.94[ASN][1000 genomes]
rs10769247	0.94[ASN][1000 genomes]
rs10838637	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838648	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10838653	0.87[EUR][1000 genomes]
rs10838655	0.81[ASN][1000 genomes]
rs10838666	0.94[ASN][1000 genomes]
rs11039054	0.87[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap]
rs11039096	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11039140	0.92[ASN][1000 genomes]
rs11039187	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11039188	0.81[ASN][1000 genomes]
rs11039193	0.83[ASN][1000 genomes]
rs11500474	0.87[EUR][1000 genomes]
rs11607346	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12419943	0.94[ASN][1000 genomes]
rs1377512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1453415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs1453417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1453418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453421	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1453426	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1840175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2123663	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs2198446	0.87[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap]
rs2343154	0.94[ASN][1000 genomes]
rs4758099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4758101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758102	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758103	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758113	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs4758427	0.94[ASN][1000 genomes]
rs4910844	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4910849	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910850	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910851	0.90[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs6578689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7484069	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs7924824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7925671	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7931236	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7935300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7937133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7938541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7940624	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7940926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7948009	0.83[CEU][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs7949986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9651658	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:58 , 50 per page) page: 1 2

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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv1055011	chr11:5770388-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	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
17	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
18	esv1806822	chr11:5778010-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv1053534	chr11:5778010-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	esv2760333	chr11:5778010-5812360	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv870386	chr11:5781977-5810039	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
22	nsv869930	chr11:5781977-5818142	Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	nsv65	chr11:5782093-5812233	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv7654	chr11:5782093-5826200	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	nsv1041014	chr11:5782913-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	esv2760180	chr11:5782925-5816285	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv1048034	chr11:5783100-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
28	esv3489668	chr11:5783376-5810374	Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
29	nsv1048993	chr11:5783383-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
30	nsv1049402	chr11:5783670-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	esv3489671	chr11:5783826-5810224	Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
32	esv2631490	chr11:5783842-5809979	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
33	nsv435927	chr11:5783884-5810228	Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
34	esv1823380	chr11:5784445-5810393	Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
35	esv1816697	chr11:5784445-5819232	Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
36	esv1818059	chr11:5784445-5819778	Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
37	nsv8784	chr11:5784483-5809778	Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
38	nsv1046530	chr11:5787393-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
39	esv3584633	chr11:5787405-5812360	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
40	nsv1053965	chr11:5788068-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
41	nsv1043847	chr11:5788068-5816285	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
42	esv3584635	chr11:5788080-5812360	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
43	nsv1049814	chr11:5789589-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
44	nsv1041139	chr11:5789589-5818321	Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
45	nsv1043371	chr11:5789713-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
46	nsv1037123	chr11:5789857-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
47	nsv1053616	chr11:5790800-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
48	nsv1041196	chr11:5790800-5829039	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
49	nsv1045542	chr11:5790951-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
50	nsv1038951	chr11:5793429-5812348	Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10742787	OR10A5	cis	cerebellum	SCAN
rs10742787	OR52N3P	cis	Adipose Subcutaneous	GTEx
rs10742787	OR51B5	cis	parietal	SCAN
rs10742787	OR52I2	cis	cerebellum	SCAN
rs10742787	RBMXL2	cis	cerebellum	SCAN
rs10742787	OR51I1	cis	parietal	SCAN
rs10742787	TRIM22	cis	parietal	SCAN
rs10742787	OR52N3P	cis	Nerve Tibial	GTEx
rs10742787	ASCL2	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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