Variant report

Variant	rs2729389
Chromosome Location	chr11:57211646-57211647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57194166..57196097-chr11:57209507..57211773,3	K562	blood:

Variant related genes	Relation type
ENSG00000134802	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11229028	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11820985	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs11822095	0.85[ASN][1000 genomes]
rs11822910	0.87[ASN][1000 genomes]
rs11827928	0.87[ASN][1000 genomes]
rs11828218	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12422015	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12788236	0.92[ASN][1000 genomes]
rs2250887	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2264054	0.82[AFR][1000 genomes]
rs2439448	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2467333	0.86[EUR][1000 genomes]
rs2511982	0.87[EUR][1000 genomes]
rs2581924	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581925	0.84[AFR][1000 genomes]
rs2581927	0.86[EUR][1000 genomes]
rs2581928	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2584858	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2729392	0.86[EUR][1000 genomes]
rs2869510	0.90[ASN][1000 genomes]
rs35677854	0.90[ASN][1000 genomes]
rs4477456	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4529894	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs61886978	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7106223	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7122734	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7943531	0.88[EUR][1000 genomes]
rs7948027	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2729389	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2729389	TIMM10	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57203800-57211800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:57206400-57212000	Weak transcription	Stomach Mucosa	stomach
3	chr11:57206800-57212000	Weak transcription	Fetal Intestine Small	intestine
4	chr11:57206800-57213200	Weak transcription	Fetal Intestine Large	intestine
5	chr11:57208400-57224600	Weak transcription	Lung	lung
6	chr11:57210200-57219000	Weak transcription	Liver	Liver
7	chr11:57211400-57211800	Enhancers	A549	lung
8	chr11:57211600-57212000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr11:57211600-57213600	Enhancers	HepG2	liver
10	chr11:57211600-57213800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr11:57211600-57214600	Enhancers	Hela-S3	cervix

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