Variant report

Variant	rs2595996
Chromosome Location	chr11:4964103-4964104
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10500624	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs11600505	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11600508	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11602621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11602673	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11824573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11826210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12786996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12787985	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12788401	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12788743	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12789377	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12791425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12794614	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs12795973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12801574	1.00[JPT][hapmap]
rs12804154	0.95[ASN][1000 genomes]
rs12807322	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12807351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12807538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17339295	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442426	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs2570576	0.80[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs2570582	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap]
rs2570583	0.80[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs2595992	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2595994	0.80[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595995	0.80[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap]
rs2595997	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2596001	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2605298	0.80[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs2605300	0.96[ASN][1000 genomes]
rs2605301	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2605302	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2605304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36049521	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945456	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:52 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2758254	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2759799	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv7652	chr11:4946245-4997769	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	nsv1052130	chr11:4948148-4974017	Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1049277	chr11:4948160-4974017	Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1036758	chr11:4948560-4974017	Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv1047179	chr11:4949956-4974017	Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1044434	chr11:4952914-4974017	Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1054610	chr11:4953844-5004203	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
11	nsv526998	chr11:4954607-5074301	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv1045154	chr11:4958462-5032685	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv540937	chr11:4958462-5032685	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
15	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
16	nsv64	chr11:4959236-4985373	Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv896918	chr11:4960032-5001570	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
18	esv1844673	chr11:4960613-4977065	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	esv1798076	chr11:4960949-4977065	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv1037222	chr11:4961506-4974017	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv1035749	chr11:4961506-4975693	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv1050555	chr11:4961506-4977070	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	nsv1043799	chr11:4961506-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
24	nsv1046196	chr11:4961506-4995448	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
25	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
26	nsv1041220	chr11:4961796-4974017	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	esv2757419	chr11:4961913-4992282	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
28	nsv508614	chr11:4962279-4971325	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
29	nsv1036425	chr11:4962632-4974017	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
30	nsv1045717	chr11:4962632-4975693	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
31	nsv1043027	chr11:4962632-4976522	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
32	nsv1046673	chr11:4962632-4976602	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
33	nsv1050051	chr11:4962632-4977070	Inactive region	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
34	nsv1039389	chr11:4962632-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
35	nsv1047355	chr11:4962933-4975693	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
36	nsv1038703	chr11:4962933-4976377	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
37	nsv1054521	chr11:4962933-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
38	nsv1040515	chr11:4963407-4975693	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
39	nsv1043268	chr11:4963407-4976602	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
40	nsv1053020	chr11:4963538-4976999	Inactive region	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
41	nsv1047698	chr11:4963552-4974017	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
42	nsv1039637	chr11:4963611-4974017	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
43	nsv1042777	chr11:4963611-4975152	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
44	nsv1045951	chr11:4963707-4974017	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
45	nsv1042446	chr11:4963707-4977070	Inactive region	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
46	nsv1037087	chr11:4963707-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
47	nsv1035565	chr11:4964103-4975152	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
48	nsv1051205	chr11:4964103-4975693	Inactive region	TF binding region	2 gene(s)	inside rSNPs	diseases
49	nsv1042273	chr11:4964103-4976602	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
50	nsv1044743	chr11:4964103-4976895	Inactive region	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2595996	OR52E6	cis	parietal	SCAN
rs2595996	OR51F2	cis	cerebellum	SCAN
rs2595996	OR5P2	cis	parietal	SCAN
rs2595996	MUC5B	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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