Variant report

Variant	rs2439448
Chromosome Location	chr11:57199211-57199212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57197604..57200405-chr11:57246413..57248386,2	K562	blood:
2	chr11:57197274..57199985-chr11:57224146..57225779,2	K562	blood:
3	chr11:57088588..57090285-chr11:57197679..57199918,2	K562	blood:

Variant related genes	Relation type
ENSG00000149115	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11229028	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820985	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11822095	1.00[ASN][1000 genomes]
rs11822910	0.98[ASN][1000 genomes]
rs11827928	0.98[ASN][1000 genomes]
rs11828218	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422015	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12788236	0.81[ASN][1000 genomes]
rs2250887	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2467333	0.81[EUR][1000 genomes]
rs2511982	0.85[EUR][1000 genomes]
rs2581924	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581927	0.87[EUR][1000 genomes]
rs2581928	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584858	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2729389	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2729392	0.87[EUR][1000 genomes]
rs4477456	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4529894	0.98[ASN][1000 genomes]
rs60961847	0.91[ASN][1000 genomes]
rs61886978	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106223	0.91[ASN][1000 genomes]
rs7122734	0.93[ASN][1000 genomes]
rs7943531	0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2439448	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57195000-57200000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:57195000-57201800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:57195000-57202400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr11:57195400-57199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:57195400-57199800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:57195400-57199800	Weak transcription	Fetal Thymus	thymus
7	chr11:57195600-57199400	Weak transcription	Brain Anterior Caudate	brain
8	chr11:57195600-57199400	Weak transcription	Spleen	Spleen
9	chr11:57195600-57199600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:57195600-57202400	Weak transcription	Pancreas	Pancrea
11	chr11:57195800-57199400	Weak transcription	Adipose Nuclei	Adipose
12	chr11:57195800-57199600	Weak transcription	Brain Substantia Nigra	brain
13	chr11:57195800-57200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:57195800-57200200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:57195800-57202000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:57195800-57202000	Weak transcription	NHEK	skin
17	chr11:57195800-57202400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:57195800-57202400	Weak transcription	Esophagus	oesophagus
19	chr11:57196000-57199400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:57196000-57199400	Weak transcription	Osteobl	bone
21	chr11:57196000-57199600	Weak transcription	HMEC	breast
22	chr11:57196000-57200000	Weak transcription	HSMM	muscle
23	chr11:57196000-57200200	Weak transcription	HSMMtube	muscle
24	chr11:57196000-57200400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:57196000-57201800	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:57196200-57199400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:57196200-57199800	Weak transcription	NHLF	lung
28	chr11:57196600-57199600	Weak transcription	NHDF-Ad	bronchial
29	chr11:57196600-57199800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:57197000-57203000	Enhancers	HepG2	liver
31	chr11:57197200-57199600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr11:57197400-57199400	Weak transcription	Lung	lung
33	chr11:57197400-57199600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:57197400-57201600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:57197600-57200000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr11:57197600-57200800	Weak transcription	Hela-S3	cervix
37	chr11:57197800-57199400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:57198200-57199400	Weak transcription	Liver	Liver
39	chr11:57198200-57199400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr11:57198200-57199800	Enhancers	K562	blood
41	chr11:57198200-57200600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:57198200-57201000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:57198200-57201800	Enhancers	A549	lung
44	chr11:57198200-57202800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:57198400-57200600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:57198400-57203000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr11:57198600-57199600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:57198600-57202600	Weak transcription	Right Atrium	heart
49	chr11:57199000-57199400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr11:57199000-57200600	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links