Variant report

Variant	rs557667
Chromosome Location	chr11:55339798-55339799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11230131	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11230173	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1459101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs2085664	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2926309	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4939359	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501880	0.80[EUR][1000 genomes]
rs504661	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs532910	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs534003	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs578067	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs660341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9804659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]

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	esv2830215	chr11:54711990-55340379	ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1052144	chr11:54720811-55438474	ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1053949	chr11:54773881-55363328	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1051643	chr11:54826801-55363328	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv524091	chr11:54875038-55522549	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv554797	chr11:55035411-55864161	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv467886	chr11:55083434-55408700	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	nsv554799	chr11:55083434-55408700	Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	nsv554800	chr11:55083434-55695985	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	nsv916012	chr11:55084067-55622531	ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
11	nsv1067779	chr11:55086995-55980406	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
12	nsv491694	chr11:55086995-55980406	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
13	nsv1036325	chr11:55119267-55442306	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island	19 gene(s)	inside rSNPs	diseases
14	esv2751031	chr11:55121706-55340753	Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island	14 gene(s)	inside rSNPs	diseases
15	nsv821668	chr11:55153930-55816828	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
16	nsv518225	chr11:55171677-55408700	ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers	TF binding region CpG island	14 gene(s)	inside rSNPs	diseases
17	esv2758271	chr11:55222420-55621884	Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
18	esv2759828	chr11:55222420-55638112	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv832154	chr11:55222427-55408933	Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island	10 gene(s)	inside rSNPs	diseases
20	nsv1046475	chr11:55241003-55381810	ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers	TF binding region CpG island	8 gene(s)	inside rSNPs	diseases
21	nsv1047882	chr11:55241003-55386385	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island	8 gene(s)	inside rSNPs	diseases
22	esv2751032	chr11:55276602-55355722	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
23	nsv832155	chr11:55277241-55432666	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island	7 gene(s)	inside rSNPs	diseases
24	nsv916314	chr11:55289861-55495986	ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv1048237	chr11:55312533-55363328	ZNF genes & repeats Bivalent Enhancer Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
26	nsv554801	chr11:55314151-55624360	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
27	nsv428256	chr11:55317076-55621884	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
28	nsv1052441	chr11:55319822-55363328	Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
29	nsv975112	chr11:55321812-55426168	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
30	nsv1046316	chr11:55322211-55435115	ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Active TSS	TF binding region CpG island	5 gene(s)	inside rSNPs	diseases
31	nsv1039064	chr11:55322211-55453564	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
32	nsv522846	chr11:55322539-55396041	ZNF genes & repeats Bivalent Enhancer Enhancers	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
33	esv2756721	chr11:55335878-55430530	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island	5 gene(s)	inside rSNPs	diseases
34	nsv916049	chr11:55337700-55450895	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS	TF binding region CpG island	7 gene(s)	inside rSNPs	diseases
35	esv2757445	chr11:55339702-55638112	ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs557667	SLC43A1	cis	parietal	SCAN
rs557667	OR5T1	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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