Variant report

Variant	rs2729394
Chromosome Location	chr11:57233567-57233568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57223855..57226276-chr11:57231482..57234003,2	K562	blood:
2	chr11:57232119..57234090-chr11:57280834..57283068,2	K562	blood:
3	chr11:57227378..57229138-chr11:57231979..57233991,2	K562	blood:
4	chr11:57232942..57235264-chr11:57237354..57240741,3	K562	blood:

Variant related genes	Relation type
ENSG00000149150	Chromatin interaction
ENSG00000186907	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1001956	0.80[ASN][1000 genomes]
rs2250673	0.82[ASN][1000 genomes]
rs2258835	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2509899	0.82[ASN][1000 genomes]
rs2511986	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2581921	0.80[ASN][1000 genomes]
rs2581922	0.80[ASN][1000 genomes]
rs2581923	0.81[EUR][1000 genomes]
rs2584856	0.80[ASN][1000 genomes]
rs2584862	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2649667	0.82[ASN][1000 genomes]
rs2729353	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2729363	0.87[EUR][1000 genomes]
rs2729384	0.82[ASN][1000 genomes]
rs2848634	0.80[EUR][1000 genomes]
rs2848635	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2848640	0.82[ASN][1000 genomes]
rs3851117	0.83[EUR][1000 genomes]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2729394	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2729394	TIMM10	cis	Heart Left Ventricle	GTEx
rs2729394	SLC43A1	cis	hippocampus	BrainEAC
rs2729394	TIMM10	cis	Artery Aorta	GTEx
rs2729394	TIMM10	cis	Artery Tibial	GTEx
rs2729394	SLC43A1	cis	brain	BrainEAC
rs2729394	TIMM10	cis	Esophagus Mucosa	GTEx
rs2729394	TIMM10	cis	Esophagus Muscularis	GTEx
rs2729394	TIMM10	cis	Thyroid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57228800-57235200	Weak transcription	Lung	lung
2	chr11:57228800-57238800	Weak transcription	Pancreas	Pancrea
3	chr11:57228800-57240000	Weak transcription	Hela-S3	cervix
4	chr11:57228800-57241600	Weak transcription	Right Atrium	heart
5	chr11:57229200-57235800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:57229800-57238200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:57230400-57240000	Weak transcription	HepG2	liver
8	chr11:57231400-57239800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:57231600-57242000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:57231800-57235200	Weak transcription	Fetal Brain Male	brain
11	chr11:57232000-57235200	Weak transcription	A549	lung
12	chr11:57232000-57240000	Weak transcription	Brain Germinal Matrix	brain
13	chr11:57232000-57240600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:57232200-57235200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:57232200-57235400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:57232200-57236000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:57232400-57235200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:57232400-57240600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr11:57232800-57235000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:57232800-57240400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr11:57233000-57234200	Enhancers	Fetal Muscle Leg	muscle
22	chr11:57233000-57235000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:57233000-57235200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:57233000-57235200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:57233000-57235200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:57233200-57235000	Weak transcription	Fetal Brain Female	brain
27	chr11:57233200-57235200	Weak transcription	Liver	Liver

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