Variant report

Variant	rs2584862
Chromosome Location	chr11:57241956-57241957
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57241042..57244897-chr11:57245318..57249265,7	K562	blood:
2	chr11:57240650..57242445-chr11:57281069..57283721,2	K562	blood:
3	chr11:57238280..57240844-chr11:57241461..57244057,2	K562	blood:
4	chr11:57240991..57243890-chr11:57248051..57250627,2	MCF-7	breast:
5	chr11:57226445..57228617-chr11:57241160..57242866,2	K562	blood:
6	chr11:57241323..57242908-chr11:57245144..57248142,2	MCF-7	breast:
7	chr11:57240605..57243296-chr11:57255789..57257513,2	K562	blood:

Variant related genes	Relation type
ENSG00000186907	Chromatin interaction
ENSG00000149150	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1001956	0.90[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2250673	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2258835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2509899	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2511986	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2581921	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2581922	0.95[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2581923	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2584856	0.95[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2649667	0.90[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2729353	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729363	0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs2729377	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2729384	0.95[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2729387	0.85[EUR][1000 genomes]
rs2729394	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2848634	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2848635	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2848640	0.95[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3851117	0.86[CEU][hapmap];0.91[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2584862	TIMM10	cis	Lymphoblastoid	GTEx
rs2584862	TIMM10	cis	Artery Aorta	GTEx
rs2584862	TIMM10	cis	Artery Tibial	GTEx
rs2584862	TIMM10	cis	Heart Left Ventricle	GTEx
rs2584862	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2584862	TIMM10	cis	Esophagus Mucosa	GTEx
rs2584862	TIMM10	cis	multi-tissue	Pritchard
rs2584862	TIMM10	cis	Frontal Cortex	GTEx
rs2584862	TIMM10	cis	lesional skin	skin_eQTL
rs2584862	TIMM10	cis	Thyroid	GTEx
rs2584862	TIMM10	cis	Temporal Cortex	GTEx
rs2584862	TIMM10	cis	Cerebellum	GTEx
rs2584862	TIMM10	cis	Brain Pons	GTEx
rs2584862	TIMM10	cis	Esophagus Muscularis	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57231600-57242000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57240200-57243400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:57240400-57244000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:57240600-57242400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:57240600-57243000	Weak transcription	Liver	Liver
6	chr11:57240600-57243400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr11:57240800-57242000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:57240800-57242000	Enhancers	Fetal Lung	lung
9	chr11:57240800-57242200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:57240800-57242400	Weak transcription	HepG2	liver
11	chr11:57240800-57242600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr11:57240800-57243400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:57240800-57243600	Bivalent Enhancer	Fetal Stomach	stomach
14	chr11:57241000-57243200	Enhancers	Primary B cells from cord blood	blood
15	chr11:57241200-57242200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:57241200-57242200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:57241200-57242200	Enhancers	Fetal Brain Male	brain
18	chr11:57241200-57242400	Enhancers	Fetal Thymus	thymus
19	chr11:57241200-57243400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr11:57241400-57242200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
21	chr11:57241400-57242200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:57241400-57242400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:57241400-57242600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr11:57241400-57242600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr11:57241400-57242600	Enhancers	Thymus	Thymus
26	chr11:57241400-57242600	Enhancers	Spleen	Spleen
27	chr11:57241400-57243200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr11:57241400-57243400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr11:57241400-57243400	Enhancers	A549	lung
30	chr11:57241400-57243600	Enhancers	Primary B cells from peripheral blood	blood
31	chr11:57241400-57243600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr11:57241600-57242000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr11:57241600-57242000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:57241600-57242000	Enhancers	Esophagus	oesophagus
35	chr11:57241600-57242000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr11:57241600-57242000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr11:57241600-57242200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
38	chr11:57241600-57242200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:57241600-57242200	Enhancers	Left Ventricle	heart
40	chr11:57241600-57242200	Genic enhancers	Right Atrium	heart
41	chr11:57241600-57242400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:57241600-57242400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:57241600-57242400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr11:57241600-57242400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:57241600-57242400	Enhancers	Pancreas	Pancrea
46	chr11:57241600-57242400	Enhancers	Hela-S3	cervix
47	chr11:57241600-57242600	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr11:57241600-57242600	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr11:57241600-57242600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:57241600-57242600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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