Variant report

Variant	rs2729384
Chromosome Location	chr11:57258617-57258618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57253056..57260530-chr11:57277596..57285007,11	K562	blood:
2	chr11:57192415..57195414-chr11:57258192..57260689,2	K562	blood:
3	chr11:57247726..57251510-chr11:57253790..57259247,6	K562	blood:
4	chr11:57254555..57260449-chr11:57262001..57269915,7	K562	blood:

Variant related genes	Relation type
ENSG00000134802	Chromatin interaction
ENSG00000149150	Chromatin interaction
ENSG00000251995	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1001956	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10750864	0.84[AMR][1000 genomes]
rs2250673	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2258835	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]
rs2467327	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2509899	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511984	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511986	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581921	0.83[ASN][1000 genomes]
rs2581922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581923	1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2584856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2584862	0.95[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2649667	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729353	1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729363	0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2729371	0.81[TSI][hapmap]
rs2729377	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729387	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729394	0.82[ASN][1000 genomes]
rs2848626	0.90[ASN][1000 genomes]
rs2848634	1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2848635	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2848640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851117	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.81[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:25)

SNP	Gene	Cis/trans	Tissue	Source
rs2729384	TIMM10	cis	Artery Aorta	GTEx
rs2729384	TIMM10	cis	lymphoblastoid	seeQTL
rs2729384	TIMM10	cis	Esophagus Muscularis	GTEx
rs2729384	TIMM10	cis	multi-tissue	Pritchard
rs2729384	TIMM10	cis	Skin Sun Exposed Lower leg	GTEx
rs2729384	TIMM10	cis	Muscle Skeletal	GTEx
rs2729384	TIMM10	cis	Esophagus Mucosa	GTEx
rs2729384	TIMM10	cis	Temporal Cortex	GTEx
rs2729384	OR5AP2	cis	parietal	SCAN
rs2729384	CMPK1	trans	parietal	SCAN
rs2729384	TIMM10	cis	Artery Tibial	GTEx
rs2729384	TIMM10	cis	Frontal Cortex	GTEx
rs2729384	SLC43A3	cis	cerebellum	SCAN
rs2729384	TIMM10	cis	Lymphoblastoid	GTEx
rs2729384	TIMM10	cis	Thyroid	GTEx
rs2729384	TIMM10	cis	Heart Left Ventricle	GTEx
rs2729384	OR10Q1	cis	parietal	SCAN
rs2729384	TIMM10	cis	Brain Pons	GTEx
rs2729384	TIMM10	cis	Cerebellum	GTEx
rs2729384	SLC43A1	cis	parietal	SCAN
rs2729384	TIMM10	cis	lesional skin	skin_eQTL
rs2729384	SLC43A1	cis	cerebellum	SCAN
rs2729384	TIMM10	cis	parietal	SCAN
rs2729384	TIMM10	cis	cerebellum	SCAN
rs2729384	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57250600-57259600	Strong transcription	Pancreas	Pancrea
2	chr11:57250800-57259600	Strong transcription	HepG2	liver
3	chr11:57250800-57266000	Weak transcription	Right Atrium	heart
4	chr11:57251000-57260600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:57251000-57261400	Weak transcription	Brain Hippocampus Middle	brain
6	chr11:57251000-57266800	Weak transcription	HUVEC	blood vessel
7	chr11:57251000-57267400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:57251200-57259600	Strong transcription	Liver	Liver
9	chr11:57251200-57260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:57251200-57260800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:57251200-57261000	Weak transcription	Brain Angular Gyrus	brain
12	chr11:57251200-57261000	Weak transcription	Dnd41	blood
13	chr11:57251200-57263800	Strong transcription	Ovary	ovary
14	chr11:57251200-57266800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:57251200-57266800	Weak transcription	HSMM	muscle
16	chr11:57251200-57280600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:57251400-57261200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:57251400-57266000	Weak transcription	Brain Substantia Nigra	brain
19	chr11:57251400-57266200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:57251400-57266400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:57251400-57266800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:57251400-57279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr11:57251400-57281200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:57251600-57258800	Strong transcription	Adipose Nuclei	Adipose
25	chr11:57251600-57259600	Strong transcription	Fetal Intestine Small	intestine
26	chr11:57251600-57259800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr11:57251600-57260800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:57251600-57266800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:57251800-57266200	Strong transcription	Fetal Stomach	stomach
30	chr11:57252000-57259200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:57252000-57259200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr11:57252000-57259200	Strong transcription	Aorta	Aorta
33	chr11:57252000-57259400	Strong transcription	Gastric	stomach
34	chr11:57252000-57260800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:57252200-57259400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:57252200-57259400	Strong transcription	Colon Smooth Muscle	Colon
37	chr11:57252200-57259400	Strong transcription	Right Ventricle	heart
38	chr11:57252200-57261000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:57252200-57261000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:57252400-57258800	Strong transcription	Fetal Intestine Large	intestine
41	chr11:57252400-57264000	Weak transcription	Stomach Mucosa	stomach
42	chr11:57252600-57258800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:57252600-57259000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr11:57252600-57267600	Weak transcription	Small Intestine	intestine
45	chr11:57252800-57266800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:57253200-57259600	Strong transcription	Spleen	Spleen
47	chr11:57253200-57266800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr11:57253200-57266800	Weak transcription	Thymus	Thymus
49	chr11:57253400-57259600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:57253400-57263200	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links