Variant report

Variant	rs488169
Chromosome Location	chr12:118808681-118808682
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118789693..118801109-chr12:118805205..118813455,21	K562	blood:
2	chr12:118765311..118767097-chr12:118807777..118809983,2	K562	blood:
3	chr12:118792933..118800473-chr12:118805927..118813309,24	K562	blood:

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs468574	0.84[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs648113	0.83[AFR][1000 genomes];0.85[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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3413770	chr12:118808569-118812117	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs488169	TBX3	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118794800-118809000	Weak transcription	Lung	lung
2	chr12:118794800-118809000	Weak transcription	Pancreas	Pancrea
3	chr12:118794800-118809200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:118794800-118809200	Weak transcription	Esophagus	oesophagus
5	chr12:118799200-118809000	Weak transcription	HSMM	muscle
6	chr12:118801800-118809000	Weak transcription	Gastric	stomach
7	chr12:118801800-118809000	Weak transcription	Left Ventricle	heart
8	chr12:118803000-118808800	Weak transcription	Right Ventricle	heart
9	chr12:118804800-118809000	Weak transcription	Spleen	Spleen
10	chr12:118806200-118809000	Weak transcription	Psoas Muscle	Psoas
11	chr12:118806600-118809000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:118806800-118809000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr12:118807000-118809200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:118807200-118809400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr12:118807200-118811400	Active TSS	NHDF-Ad	bronchial
16	chr12:118807600-118808800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:118807800-118808800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:118808000-118808800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
19	chr12:118808000-118808800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:118808000-118808800	Flanking Active TSS	GM12878-XiMat	blood
21	chr12:118808000-118809000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:118808000-118809000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:118808000-118809200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:118808000-118809400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr12:118808000-118811400	Active TSS	NHLF	lung
26	chr12:118808200-118808800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
27	chr12:118808200-118808800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:118808200-118808800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:118808200-118808800	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr12:118808200-118809000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr12:118808200-118809200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:118808200-118809600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:118808200-118810000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:118808400-118808800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr12:118808400-118808800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
36	chr12:118808400-118808800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:118808400-118808800	Bivalent Enhancer	Primary B cells from cord blood	blood
38	chr12:118808400-118808800	Enhancers	Primary T cells from cord blood	blood
39	chr12:118808400-118808800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr12:118808400-118808800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr12:118808400-118808800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:118808400-118808800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:118808400-118808800	Enhancers	Colon Smooth Muscle	Colon
44	chr12:118808400-118808800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr12:118808400-118808800	Flanking Active TSS	Fetal Lung	lung
46	chr12:118808400-118808800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr12:118808400-118808800	Flanking Active TSS	HepG2	liver
48	chr12:118808400-118808800	Flanking Active TSS	HMEC	breast
49	chr12:118808400-118809000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr12:118808400-118809000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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