Variant report

Variant	rs2509899
Chromosome Location	chr11:57262596-57262597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57262197..57265098-chr11:57268872..57270769,2	K562	blood:
2	chr11:57260621..57264536-chr11:57264640..57268839,7	K562	blood:
3	chr11:57260838..57262632-chr11:57281221..57283072,2	K562	blood:
4	chr11:57260706..57264705-chr11:57283186..57286169,4	K562	blood:

Variant related genes	Relation type
ENSG00000149150	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1001956	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10750864	0.81[AMR][1000 genomes]
rs2250673	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2258835	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2467327	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511984	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511986	0.91[ASN][1000 genomes]
rs2581921	0.83[ASN][1000 genomes]
rs2581922	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581923	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2584856	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2584862	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2649667	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729353	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729363	0.80[ASN][1000 genomes]
rs2729377	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729384	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729387	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729394	0.82[ASN][1000 genomes]
rs2848626	0.90[ASN][1000 genomes]
rs2848634	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2848635	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2848640	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs2509899	TIMM10	cis	Muscle Skeletal	GTEx
rs2509899	TIMM10	cis	Esophagus Muscularis	GTEx
rs2509899	TIMM10	cis	Artery Tibial	GTEx
rs2509899	TIMM10	cis	Artery Aorta	GTEx
rs2509899	TIMM10	cis	Heart Left Ventricle	GTEx
rs2509899	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2509899	TIMM10	cis	Skin Sun Exposed Lower leg	GTEx
rs2509899	TIMM10	cis	Esophagus Mucosa	GTEx
rs2509899	TIMM10	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57250800-57266000	Weak transcription	Right Atrium	heart
2	chr11:57251000-57266800	Weak transcription	HUVEC	blood vessel
3	chr11:57251000-57267400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:57251200-57263800	Strong transcription	Ovary	ovary
5	chr11:57251200-57266800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:57251200-57266800	Weak transcription	HSMM	muscle
7	chr11:57251200-57280600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:57251400-57266000	Weak transcription	Brain Substantia Nigra	brain
9	chr11:57251400-57266200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:57251400-57266400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:57251400-57266800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:57251400-57279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:57251400-57281200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:57251600-57266800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr11:57251800-57266200	Strong transcription	Fetal Stomach	stomach
16	chr11:57252400-57264000	Weak transcription	Stomach Mucosa	stomach
17	chr11:57252600-57267600	Weak transcription	Small Intestine	intestine
18	chr11:57252800-57266800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:57253200-57266800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:57253200-57266800	Weak transcription	Thymus	Thymus
21	chr11:57253400-57263200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:57253400-57266800	Weak transcription	Fetal Thymus	thymus
23	chr11:57253800-57266800	Weak transcription	Colonic Mucosa	Colon
24	chr11:57253800-57266800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:57253800-57266800	Weak transcription	Osteobl	bone
26	chr11:57253800-57276400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:57253800-57279000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:57255200-57266800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:57255200-57269600	Weak transcription	Esophagus	oesophagus
30	chr11:57256000-57266800	Weak transcription	HSMMtube	muscle
31	chr11:57256400-57273000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:57256800-57266800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:57257000-57267800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:57257200-57266600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:57257400-57281400	Weak transcription	Primary T cells from cord blood	blood
36	chr11:57258000-57266800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:57258600-57266800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr11:57258800-57266800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr11:57258800-57266800	Weak transcription	NHDF-Ad	bronchial
40	chr11:57258800-57279200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:57259000-57263400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr11:57259000-57267800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:57259200-57264000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr11:57259200-57266200	Weak transcription	Left Ventricle	heart
45	chr11:57259200-57266400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:57259200-57266800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:57259200-57267200	Weak transcription	Aorta	Aorta
48	chr11:57259200-57279000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr11:57259200-57280800	Weak transcription	GM12878-XiMat	blood
50	chr11:57259400-57263000	Weak transcription	Lung	lung

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