Variant report

Variant	rs633129
Chromosome Location	chr11:57685196-57685197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

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];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs11229109	0.81[YRI][hapmap]
rs11229170	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11229171	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11229172	0.86[AMR][1000 genomes];0.93[EUR][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];0.82[MEX][hapmap];0.84[YRI][hapmap]
rs11570181	0.85[ASW][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];0.82[MEX][hapmap];0.84[YRI][hapmap]
rs2956981	0.82[MEX][hapmap]
rs3017889	0.82[MEX][hapmap]
rs36036499	0.85[ASW][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs4245215	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs588713	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588808	0.98[ASN][1000 genomes]
rs591322	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592785	0.84[ASN][1000 genomes]
rs593239	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs600488	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602861	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs606731	0.94[EUR][1000 genomes]
rs615133	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]
rs616911	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626043	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs627145	0.82[MEX][hapmap]
rs636388	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs652191	0.84[YRI][hapmap]
rs653889	0.85[ASW][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];0.93[ASN][1000 genomes]
rs665058	0.82[MEX][hapmap]
rs681397	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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];0.84[YRI][hapmap]
rs7926999	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7943793	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs633129	OR4C6	cis	parietal	SCAN
rs633129	TIMM10	cis	parietal	SCAN
rs633129	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs633129	TIMM10	cis	multi-tissue	Pritchard
rs633129	OR4D11	cis	parietal	SCAN
rs633129	YPEL4	cis	lung	GTEx
rs633129	MS4A2	cis	cerebellum	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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