Variant report

Variant	rs2729377
Chromosome Location	chr11:57250084-57250085
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57249957..57251485-chr11:57254950..57256797,2	MCF-7	breast:
2	chr11:57248959..57251782-chr11:57265307..57267262,2	MCF-7	breast:
3	chr11:57249684..57251719-chr11:57280040..57282161,2	K562	blood:
4	chr11:57247726..57251510-chr11:57253790..57259247,6	K562	blood:
5	chr11:57246699..57250241-chr11:57294566..57299733,5	K562	blood:
6	chr11:57240991..57243890-chr11:57248051..57250627,2	MCF-7	breast:
7	chr11:57244323..57249361-chr11:57249933..57253488,6	K562	blood:
8	chr11:57249212..57250918-chr11:57265410..57267612,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134809	Chromatin interaction
ENSG00000255301	Chromatin interaction
ENSG00000149150	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1001956	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250673	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2258835	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2467327	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2509899	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2511984	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2511986	0.84[ASN][1000 genomes]
rs2581921	0.80[ASN][1000 genomes]
rs2581922	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581923	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2584856	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2584862	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2649667	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729353	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2729384	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729387	0.88[EUR][1000 genomes]
rs2848634	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2848635	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2848640	0.89[EUR][1000 genomes];0.84[ASN][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
rs2729377	TIMM10	cis	Muscle Skeletal	GTEx
rs2729377	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2729377	TIMM10	cis	Heart Left Ventricle	GTEx
rs2729377	TIMM10	cis	Thyroid	GTEx
rs2729377	TIMM10	cis	Artery Tibial	GTEx
rs2729377	TIMM10	cis	Esophagus Muscularis	GTEx
rs2729377	TIMM10	cis	multi-tissue	Pritchard
rs2729377	TIMM10	cis	Artery Aorta	GTEx
rs2729377	TIMM10	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57244000-57250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:57244600-57250400	Enhancers	Liver	Liver
3	chr11:57244600-57250400	Weak transcription	Right Atrium	heart
4	chr11:57245600-57250600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:57247200-57250400	Weak transcription	GM12878-XiMat	blood
6	chr11:57247200-57250600	Weak transcription	Gastric	stomach
7	chr11:57247200-57250600	Weak transcription	Pancreas	Pancrea
8	chr11:57248400-57250200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:57248600-57252200	Weak transcription	K562	blood
10	chr11:57248800-57250400	Enhancers	Fetal Brain Male	brain
11	chr11:57248800-57252000	Weak transcription	Aorta	Aorta
12	chr11:57249000-57250800	Weak transcription	HepG2	liver
13	chr11:57249200-57250200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr11:57249200-57250200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr11:57249200-57250400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr11:57249400-57250400	Bivalent Enhancer	Fetal Thymus	thymus
17	chr11:57249400-57250800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr11:57249600-57250200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:57249600-57250200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:57249600-57250200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
21	chr11:57249600-57250400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:57249600-57250400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr11:57249600-57250600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:57249600-57250800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr11:57249600-57250800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr11:57249600-57250800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr11:57249600-57250800	Active TSS	Fetal Brain Female	brain
28	chr11:57249600-57251000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr11:57249600-57251000	Active TSS	H9 Cell Line	embryonic stem cell
30	chr11:57249600-57251000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
31	chr11:57249600-57251000	Enhancers	Spleen	Spleen
32	chr11:57249600-57251200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:57249600-57251400	Enhancers	Lung	lung
34	chr11:57249800-57250200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:57249800-57250200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
36	chr11:57249800-57250200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
37	chr11:57249800-57250200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:57249800-57250200	Bivalent Enhancer	Fetal Intestine Small	intestine
39	chr11:57249800-57250200	Bivalent Enhancer	Psoas Muscle	Psoas
40	chr11:57249800-57250400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:57249800-57250400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:57249800-57250400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:57249800-57250400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr11:57249800-57250400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:57249800-57250400	Bivalent Enhancer	Adipose Nuclei	Adipose
46	chr11:57249800-57250400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr11:57249800-57250600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:57249800-57250600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
49	chr11:57249800-57250600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:57249800-57250800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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