Variant report

Variant	rs2729363
Chromosome Location	chr11:57226854-57226855
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr11:57226831-57228112	K562	blood:	n/a	chr11:57227412-57227421 chr11:57227412-57227421 chr11:57227410-57227423 chr11:57227406-57227427 chr11:57227413-57227422
2	ZBTB7A	chr11:57226714-57227002	K562	blood:	n/a	n/a
3	GATA1	chr11:57226802-57227227	PBDE	blood:	n/a	chr11:57227178-57227185 chr11:57227176-57227185
4	POLR2A	chr11:57226348-57233292	HepG2	liver:	n/a	n/a
5	BACH1	chr11:57224572-57227161	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAZ	chr11:57225891-57228460	IMR90	lung:	n/a	chr11:57227422-57227432
7	HMGN3	chr11:57226677-57227119	K562	blood:	n/a	n/a
8	MAX	chr11:57226761-57228248	A549	lung:	n/a	chr11:57227422-57227432
9	ZNF263	chr11:57226181-57227669	HEK293-T-REx	kidney:	n/a	chr11:57226446-57226467
10	CTCF	chr11:57226760-57226910	GM12865	blood:	n/a	n/a
11	CTCF	chr11:57226800-57226950	HUVEC	blood vessel:	n/a	n/a
12	CCNT2	chr11:57226743-57227088	K562	blood:	n/a	chr11:57226866-57226875
13	UBTF	chr11:57226290-57227223	K562	blood:	n/a	n/a
14	POLR2A	chr11:57225985-57231748	Hela-S3	cervix:	n/a	n/a
15	SIN3A	chr11:57224662-57229214	H1-hESC	embryonic stem cell:	n/a	chr11:57227668-57227679 chr11:57228385-57228396 chr11:57227614-57227627 chr11:57226987-57226998 chr11:57229130-57229140 chr11:57228095-57228108 chr11:57225911-57225922 chr11:57224989-57225003 chr11:57228080-57228089
16	BHLHE40	chr11:57226739-57227983	GM12878	blood:	n/a	chr11:57227412-57227421 chr11:57227412-57227421 chr11:57227410-57227423 chr11:57227406-57227427 chr11:57226767-57226783 chr11:57227413-57227422
17	SUZ12	chr11:57226257-57227677	NT2-D1	testis:	n/a	n/a
18	CTBP2	chr11:57226138-57227195	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57225843..57227137-chr11:57260517..57261378,3	MCF-7	breast:
2	chr11:57224499..57227061-chr11:57335779..57338545,2	K562	blood:
3	chr11:57225401..57228536-chr11:57297717..57300309,4	K562	blood:
4	chr11:57225355..57227586-chr11:57244196..57245720,2	MCF-7	breast:
5	chr11:57224684..57228396-chr11:57412206..57415806,3	K562	blood:
6	chr11:57224897..57227312-chr11:57294275..57298279,5	MCF-7	breast:
7	chr11:57225876..57227114-chr11:57294349..57295273,7	K562	blood:
8	chr11:57226847..57229273-chr11:57333715..57336392,3	K562	blood:

Variant related genes	Relation type
RTN4RL2	TF binding region
ENSG00000134809	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000255301	Chromatin interaction
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1001956	0.91[JPT][hapmap]
rs2250673	0.80[ASN][1000 genomes]
rs2258835	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2509899	0.80[ASN][1000 genomes]
rs2511986	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581921	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2581922	1.00[JPT][hapmap]
rs2581923	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2584856	1.00[JPT][hapmap]
rs2584862	0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs2649667	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2729353	0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2729384	0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2729394	0.87[EUR][1000 genomes]
rs2848634	0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2848635	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2848640	0.80[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3851117	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2729363	TIMM10	cis	Artery Tibial	GTEx
rs2729363	TIMM10	cis	multi-tissue	Pritchard
rs2729363	TIMM10	cis	Esophagus Muscularis	GTEx
rs2729363	TIMM10	cis	Artery Aorta	GTEx
rs2729363	TIMM10	cis	Thyroid	GTEx
rs2729363	TIMM10	cis	Esophagus Mucosa	GTEx
rs2729363	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57224600-57227000	Bivalent Enhancer	Placenta	Placenta
2	chr11:57224800-57229400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:57225400-57227000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr11:57225400-57227600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr11:57225400-57227800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:57225400-57229200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr11:57225600-57227000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr11:57225600-57227000	Bivalent/Poised TSS	Fetal Brain Female	brain
9	chr11:57225600-57227800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:57225600-57227800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
11	chr11:57225600-57227800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:57225600-57227800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr11:57225600-57228000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
14	chr11:57225600-57229000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr11:57225600-57229200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr11:57225800-57227800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:57226000-57227000	Bivalent/Poised TSS	Esophagus	oesophagus
18	chr11:57226000-57227200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
19	chr11:57226000-57227600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
20	chr11:57226000-57227600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
21	chr11:57226000-57227800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
22	chr11:57226000-57227800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:57226000-57227800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:57226000-57227800	Flanking Active TSS	Liver	Liver
25	chr11:57226000-57228000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
26	chr11:57226000-57228800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
27	chr11:57226200-57227200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
28	chr11:57226200-57227600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
29	chr11:57226200-57227600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:57226200-57227600	Flanking Active TSS	Pancreas	Pancrea
31	chr11:57226200-57227800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:57226200-57227800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
33	chr11:57226200-57227800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
34	chr11:57226200-57227800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr11:57226200-57227800	Flanking Active TSS	K562	blood
36	chr11:57226200-57227800	Flanking Bivalent TSS/Enh	NHEK	skin
37	chr11:57226200-57228800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:57226400-57227000	Flanking Active TSS	Ovary	ovary
39	chr11:57226400-57227000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
40	chr11:57226400-57227000	Flanking Bivalent TSS/Enh	HMEC	breast
41	chr11:57226400-57227000	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
42	chr11:57226400-57227200	Flanking Bivalent TSS/Enh	Osteobl	bone
43	chr11:57226400-57227400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr11:57226400-57227400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:57226400-57227400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:57226400-57227400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:57226400-57227400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
48	chr11:57226400-57227400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr11:57226400-57227400	Bivalent Enhancer	Fetal Stomach	stomach
50	chr11:57226400-57227400	Flanking Bivalent TSS/Enh	A549	lung

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