Variant report

Variant	rs2258835
Chromosome Location	chr11:57243588-57243589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57243051..57244044-chr3:51976563..51977136,2	Hela-S3	cervix:
2	chr11:57241042..57244897-chr11:57245318..57249265,7	K562	blood:
3	chr11:57243239..57245827-chr11:57433789..57436480,2	K562	blood:
4	chr11:57238280..57240844-chr11:57241461..57244057,2	K562	blood:
5	chr11:57243206..57244051-chr15:66796884..66797509,2	Hela-S3	cervix:
6	chr11:57227567..57231399-chr11:57243101..57246842,4	MCF-7	breast:
7	chr11:57240991..57243890-chr11:57248051..57250627,2	MCF-7	breast:
8	chr11:57242576..57245304-chr11:57423792..57425526,2	MCF-7	breast:
9	chr11:57227974..57230199-chr11:57243067..57246052,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186907	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000174444	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000174442	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001956	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250673	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2467327	0.83[ASN][1000 genomes]
rs2509899	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2511984	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2511986	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2581921	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581922	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581923	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2584856	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2584862	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]
rs2649667	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729353	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729363	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2729377	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729384	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729387	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2729394	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2848626	0.80[ASN][1000 genomes]
rs2848634	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2848635	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848640	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851117	0.86[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv3404360	chr11:57242601-57245149	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2258835	TIMM10	cis	Heart Left Ventricle	GTEx
rs2258835	TIMM10	cis	Thyroid	GTEx
rs2258835	TIMM10	cis	multi-tissue	Pritchard
rs2258835	TIMM10	cis	Artery Tibial	GTEx
rs2258835	TIMM10	cis	Brain Pons	GTEx
rs2258835	TIMM10	cis	Cerebellum	GTEx
rs2258835	TIMM10	cis	Artery Aorta	GTEx
rs2258835	TIMM10	cis	Esophagus Mucosa	GTEx
rs2258835	TIMM10	cis	lesional skin	skin_eQTL
rs2258835	TIMM10	cis	Temporal Cortex	GTEx
rs2258835	TIMM10	cis	Lymphoblastoid	GTEx
rs2258835	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2258835	TIMM10	cis	Frontal Cortex	GTEx
rs2258835	TIMM10	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57240400-57244000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr11:57240800-57243600	Bivalent Enhancer	Fetal Stomach	stomach
3	chr11:57241400-57243600	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:57241400-57243600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr11:57241600-57243600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr11:57241600-57243600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr11:57241800-57243600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:57242000-57244400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:57242000-57244800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:57242200-57243600	Enhancers	Primary hematopoietic stem cells	blood
11	chr11:57242200-57244400	Bivalent Enhancer	Fetal Brain Male	brain
12	chr11:57242200-57246400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:57242400-57243800	Flanking Active TSS	Hela-S3	cervix
14	chr11:57242400-57244200	Bivalent Enhancer	Fetal Thymus	thymus
15	chr11:57242600-57243600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr11:57242600-57243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:57242600-57243600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr11:57242600-57243600	Bivalent Enhancer	Thymus	Thymus
19	chr11:57242600-57244600	Flanking Active TSS	GM12878-XiMat	blood
20	chr11:57242800-57243600	Bivalent Enhancer	NHEK	skin
21	chr11:57242800-57243800	Bivalent Enhancer	HUVEC	blood vessel
22	chr11:57242800-57245200	Weak transcription	HepG2	liver
23	chr11:57242800-57247600	Weak transcription	K562	blood
24	chr11:57243000-57243600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:57243000-57243600	Enhancers	Liver	Liver
26	chr11:57243200-57243600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
27	chr11:57243200-57243600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:57243200-57243600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:57243200-57243600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr11:57243200-57243600	Bivalent Enhancer	Adipose Nuclei	Adipose
31	chr11:57243200-57243600	Bivalent Enhancer	Colon Smooth Muscle	Colon
32	chr11:57243200-57243600	Enhancers	Esophagus	oesophagus
33	chr11:57243200-57243600	Bivalent Enhancer	Fetal Intestine Small	intestine
34	chr11:57243200-57243600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr11:57243200-57243600	Enhancers	Left Ventricle	heart
36	chr11:57243200-57243600	Enhancers	Psoas Muscle	Psoas
37	chr11:57243200-57243800	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr11:57243200-57243800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr11:57243200-57244600	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr11:57243200-57244600	Bivalent Enhancer	Fetal Heart	heart
41	chr11:57243200-57244600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
42	chr11:57243200-57244800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr11:57243200-57244800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:57243400-57243600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
45	chr11:57243400-57243600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:57243400-57243600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
47	chr11:57243400-57243600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr11:57243400-57243600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
49	chr11:57243400-57243600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr11:57243400-57243600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood

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