Variant report

Variant	rs2657173
Chromosome Location	chr11:4562458-4562459
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 165 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10500603	0.84[ASN][1000 genomes]
rs10836172	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10836177	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs10836245	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10836246	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10836247	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10836248	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11032545	0.85[ASN][1000 genomes]
rs11032547	0.86[ASN][1000 genomes]
rs11032710	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11032757	0.99[ASN][1000 genomes]
rs12224815	0.96[ASN][1000 genomes]
rs12225750	0.89[ASN][1000 genomes]
rs12279728	0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs1394718	0.81[ASN][1000 genomes]
rs1394719	0.83[ASN][1000 genomes]
rs1394720	0.83[ASN][1000 genomes]
rs1430397	0.84[ASN][1000 genomes]
rs1430402	0.85[ASN][1000 genomes]
rs1430403	0.85[ASN][1000 genomes]
rs1505216	0.92[ASN][1000 genomes]
rs1605028	0.89[ASN][1000 genomes]
rs16911356	0.84[ASN][1000 genomes]
rs184543	0.81[ASN][1000 genomes]
rs186694	0.84[ASN][1000 genomes]
rs2115932	0.84[ASN][1000 genomes]
rs2163286	0.84[ASN][1000 genomes]
rs2252060	0.85[ASN][1000 genomes]
rs2252061	0.85[ASN][1000 genomes]
rs230549	0.83[ASN][1000 genomes]
rs2435538	0.85[ASN][1000 genomes]
rs2435539	0.85[ASN][1000 genomes]
rs2435540	0.85[ASN][1000 genomes]
rs2435541	0.85[ASN][1000 genomes]
rs2435542	0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs2464928	0.82[ASN][1000 genomes]
rs2464931	0.85[ASN][1000 genomes]
rs2566200	0.89[ASN][1000 genomes]
rs2566201	0.89[ASN][1000 genomes]
rs2566202	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2566203	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs2566205	0.81[JPT][hapmap]
rs2566208	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2566211	0.84[JPT][hapmap]
rs2566213	0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2566214	0.86[ASN][1000 genomes]
rs2566215	0.87[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs2566217	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2566218	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2566219	0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2566221	0.87[ASN][1000 genomes]
rs2566222	0.87[ASN][1000 genomes]
rs2566223	0.87[ASN][1000 genomes]
rs2566224	0.87[ASN][1000 genomes]
rs2566225	0.87[ASN][1000 genomes]
rs2566226	0.87[ASN][1000 genomes]
rs2566227	0.87[ASN][1000 genomes]
rs2566228	0.87[ASN][1000 genomes]
rs2566229	0.87[ASN][1000 genomes]
rs2566231	0.87[ASN][1000 genomes]
rs2566232	0.82[ASN][1000 genomes]
rs2566235	0.86[ASN][1000 genomes]
rs2566236	0.85[ASN][1000 genomes]
rs2566237	0.85[ASN][1000 genomes]
rs2566238	0.85[ASN][1000 genomes]
rs2566239	0.85[ASN][1000 genomes]
rs2566240	0.85[ASN][1000 genomes]
rs2566242	0.85[ASN][1000 genomes]
rs2566243	0.84[ASN][1000 genomes]
rs2566244	0.85[ASN][1000 genomes]
rs2566245	0.85[ASN][1000 genomes]
rs2566246	0.85[ASN][1000 genomes]
rs2566247	0.85[ASN][1000 genomes]
rs2566248	0.85[ASN][1000 genomes]
rs2566269	0.99[ASN][1000 genomes]
rs2566271	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566272	0.85[JPT][hapmap]
rs2566273	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2641407	0.85[ASN][1000 genomes]
rs2641409	0.99[ASN][1000 genomes]
rs2641412	0.85[JPT][hapmap];0.89[MEX][hapmap]
rs2641413	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641414	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2657147	0.84[ASN][1000 genomes]
rs2657167	0.85[JPT][hapmap]
rs2657168	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2657169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657170	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2657174	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];0.99[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs2657175	0.85[JPT][hapmap];0.89[MEX][hapmap]
rs2657176	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657177	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657178	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs2657179	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657180	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657186	0.84[ASN][1000 genomes]
rs2657187	0.84[ASN][1000 genomes]
rs2709127	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2709128	0.84[ASN][1000 genomes]
rs2709129	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2709131	0.91[ASN][1000 genomes]
rs2709133	0.89[ASN][1000 genomes]
rs2709137	0.85[ASN][1000 genomes]
rs2709138	0.85[ASN][1000 genomes]
rs2709139	0.85[ASN][1000 genomes]
rs2709140	0.85[ASN][1000 genomes]
rs2709141	0.85[ASN][1000 genomes]
rs2709142	0.85[ASN][1000 genomes]
rs2709143	0.85[ASN][1000 genomes]
rs2709144	0.85[ASN][1000 genomes]
rs2709145	0.85[ASN][1000 genomes]
rs2709146	0.83[ASN][1000 genomes]
rs2709147	0.85[ASN][1000 genomes]
rs2709150	0.85[ASN][1000 genomes]
rs2709152	0.86[ASN][1000 genomes]
rs2709153	0.82[ASN][1000 genomes]
rs2709154	0.82[ASN][1000 genomes]
rs2709156	0.87[ASN][1000 genomes]
rs2709159	0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2709160	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs2709164	0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap]
rs2709170	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2709173	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709174	0.92[ASN][1000 genomes]
rs2709182	0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs2709185	0.85[JPT][hapmap]
rs2709187	0.84[ASN][1000 genomes]
rs2898960	0.85[ASN][1000 genomes]
rs2915049	0.85[ASN][1000 genomes]
rs2938834	0.83[ASN][1000 genomes]
rs331509	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs331510	0.82[ASN][1000 genomes]
rs331515	0.83[ASN][1000 genomes]
rs331517	0.83[ASN][1000 genomes]
rs331518	0.82[ASN][1000 genomes]
rs4343016	0.84[ASN][1000 genomes]
rs4910628	0.84[ASN][1000 genomes]
rs7101688	0.84[ASN][1000 genomes]
rs7113602	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043803	chr11:4388448-4837042	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv540916	chr11:4388448-4837042	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv553159	chr11:4389110-4599221	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1048224	chr11:4390227-4920324	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	nsv540917	chr11:4390227-4920324	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
6	nsv896911	chr11:4400801-4806872	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv553160	chr11:4404192-4589567	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv553161	chr11:4404192-4589780	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv2757418	chr11:4510285-4562458	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2759798	chr11:4510285-4562458	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv896912	chr11:4516365-4578530	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv896913	chr11:4516365-4589780	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1052736	chr11:4519302-4635855	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	nsv540921	chr11:4519302-4635855	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
15	nsv1039206	chr11:4524438-4582150	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv1047344	chr11:4524493-4630740	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
17	esv2753185	chr11:4526374-4576395	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	esv3693387	chr11:4527196-4573236	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	esv2751024	chr11:4535321-4578714	Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	esv2762892	chr11:4541825-4619236	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
21	nsv1042142	chr11:4542923-4573320	Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv540922	chr11:4542923-4573320	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1044093	chr11:4544058-4588414	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv1050498	chr11:4546300-4573642	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv832055	chr11:4550894-4736340	Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	nsv1047280	chr11:4559233-4585036	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2657173	OR51D1	cis	cerebellum	SCAN
rs2657173	OR56B1	cis	cerebellum	SCAN
rs2657173	OR51B4	cis	cerebellum	SCAN
rs2657173	OR52K2	cis	multi-tissue	Pritchard
rs2657173	PGAP2	cis	cerebellum	SCAN
rs2657173	C11orf21	cis	parietal	SCAN
rs2657173	TRPC2	cis	cerebellum	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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