Variant report

Variant	rs615133
Chromosome Location	chr11:57684949-57684950
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10750870	0.87[MEX][hapmap]
rs10792118	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10896644	0.85[ASW][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs11229109	0.81[YRI][hapmap]
rs11229170	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11229171	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11229172	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11229173	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229183	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11570176	0.85[ASW][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[YRI][hapmap]
rs11570181	0.85[ASW][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[YRI][hapmap]
rs12366063	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12420220	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17455422	0.85[ASW][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[YRI][hapmap]
rs2956981	0.82[MEX][hapmap]
rs3017889	0.82[MEX][hapmap]
rs36036499	0.85[ASW][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs4245215	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs588713	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588808	0.96[ASN][1000 genomes]
rs591322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs592785	0.83[ASN][1000 genomes]
rs593239	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs600488	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs602861	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs606731	0.94[EUR][1000 genomes]
rs616911	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs626043	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs627145	0.82[MEX][hapmap]
rs633129	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636388	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs652191	0.84[YRI][hapmap]
rs653889	0.85[ASW][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs6591443	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs662638	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs665058	0.82[MEX][hapmap]
rs681397	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7103977	0.81[EUR][1000 genomes]
rs7117020	0.82[MEX][hapmap]
rs7119973	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7120868	0.85[ASW][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap]
rs7926999	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7943793	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs615133	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs615133	OR4D11	cis	parietal	SCAN
rs615133	YPEL4	cis	lung	GTEx
rs615133	TIMM10	cis	parietal	SCAN
rs615133	MS4A2	cis	cerebellum	SCAN
rs615133	OR4C6	cis	parietal	SCAN

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57680000-57687800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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