Variant report

Variant	rs12954686
Chromosome Location	chr18:12336047-12336048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12304979..12308873-chr18:12332783..12336926,3	K562	blood:
2	chr18:12307373..12309147-chr18:12335426..12337679,2	K562	blood:
3	chr18:12313329..12315227-chr18:12335610..12338278,2	K562	blood:
4	chr18:12309313..12312439-chr18:12334613..12337209,3	MCF-7	breast:
5	chr18:12333547..12336346-chr18:12375267..12377221,2	K562	blood:
6	chr18:12330971..12332498-chr18:12334634..12336451,2	K562	blood:
7	chr18:12327171..12330634-chr18:12335563..12338039,3	K562	blood:
8	chr18:12334246..12336186-chr18:12342528..12345170,2	K562	blood:
9	chr18:12308133..12311040-chr18:12335437..12337755,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10459999	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10460000	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10460001	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10853225	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11080564	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11080565	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11080569	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11080571	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11080572	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1129115	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11553521	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11662523	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11664216	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11665134	0.87[AMR][1000 genomes]
rs11875938	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12455273	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12456857	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12604732	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12968089	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12968566	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1547858	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1941222	0.80[EUR][1000 genomes]
rs2298542	0.81[EUR][1000 genomes]
rs2298543	0.81[EUR][1000 genomes]
rs2509510	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28372882	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34829762	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3786260	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs478088	0.83[EUR][1000 genomes]
rs4796961	0.89[AMR][1000 genomes]
rs4796964	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4797677	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4797680	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs553091	0.83[EUR][1000 genomes]
rs566960	0.83[EUR][1000 genomes]
rs62098961	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs693449	0.83[EUR][1000 genomes]
rs7231182	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7231409	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7235237	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7235296	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7407640	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7504908	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7504974	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8086821	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8086993	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8087840	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8092506	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8097342	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303769	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303771	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9635829	0.81[EUR][1000 genomes]
rs9946698	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9951945	0.80[AMR][1000 genomes]
rs9960103	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9964406	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12954686	TUBB6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12314400-12342600	Weak transcription	Small Intestine	intestine
2	chr18:12319000-12336800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr18:12320800-12348200	Strong transcription	Fetal Intestine Small	intestine
4	chr18:12323400-12342800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr18:12324800-12337000	Strong transcription	Liver	Liver
6	chr18:12324800-12338800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr18:12324800-12339400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr18:12326000-12343200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr18:12326200-12366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr18:12329600-12336800	Weak transcription	NHDF-Ad	bronchial
11	chr18:12331400-12336800	Weak transcription	HUVEC	blood vessel
12	chr18:12333000-12336400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr18:12333000-12336800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr18:12333200-12336200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr18:12333200-12339600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr18:12333200-12362200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr18:12333400-12336400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr18:12333400-12336400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr18:12333400-12337000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr18:12333400-12339000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr18:12333400-12339000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr18:12333400-12339000	Strong transcription	Colonic Mucosa	Colon
25	chr18:12333400-12339200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr18:12333400-12339600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr18:12333400-12339600	Strong transcription	Thymus	Thymus
28	chr18:12333400-12340800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr18:12333400-12366600	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
31	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
32	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
33	chr18:12333600-12336200	Strong transcription	Brain Angular Gyrus	brain
34	chr18:12333600-12336400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:12333600-12336400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:12333600-12336400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr18:12333600-12336400	Strong transcription	Fetal Lung	lung
38	chr18:12333600-12336400	Strong transcription	NHLF	lung
39	chr18:12333600-12336800	Strong transcription	GM12878-XiMat	blood
40	chr18:12333600-12336800	Strong transcription	Hela-S3	cervix
41	chr18:12333600-12336800	Strong transcription	HSMM	muscle
42	chr18:12333600-12336800	Strong transcription	Osteobl	bone
43	chr18:12333600-12337400	Genic enhancers	Fetal Heart	heart
44	chr18:12333600-12337400	Strong transcription	K562	blood
45	chr18:12333600-12338600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr18:12333600-12338600	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr18:12333600-12338600	Strong transcription	Ovary	ovary
48	chr18:12333600-12338600	Strong transcription	Spleen	Spleen
49	chr18:12333600-12338800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr18:12333600-12339000	Strong transcription	Dnd41	blood

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