Variant report

Variant	rs3819091
Chromosome Location	chr18:12364185-12364186
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12363842-12364492	HepG2	liver:	n/a	n/a
2	POLR2A	chr18:12364178-12364326	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12362548..12366829-chr18:12375336..12378234,6	MCF-7	breast:
2	chr18:12336416..12339580-chr18:12362136..12364689,3	K562	blood:
3	chr18:12362726..12365078-chr18:12367506..12369159,2	MCF-7	breast:
4	chr18:12360384..12361889-chr18:12363485..12365127,2	K562	blood:
5	chr18:12308206..12311598-chr18:12363636..12368476,4	K562	blood:

No data

Variant related genes	Relation type
AFG3L2	TF binding region
ENSG00000141385	Chromatin interaction
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11659246	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs11660106	0.85[ASN][1000 genomes]
rs11661684	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11661708	0.95[ASN][1000 genomes]
rs11662319	1.00[CEU][hapmap]
rs11663340	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs11664255	0.85[ASN][1000 genomes]
rs11664282	0.85[ASN][1000 genomes]
rs11665201	1.00[CEU][hapmap]
rs11872615	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11873521	1.00[CEU][hapmap]
rs12327346	0.92[ASN][1000 genomes]
rs12960267	0.85[CHB][hapmap]
rs16977167	1.00[CEU][hapmap]
rs28470464	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28823942	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796963	0.85[CHB][hapmap]
rs541016	1.00[CEU][hapmap]
rs6416994	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7231304	0.93[CHB][hapmap];0.89[ASN][1000 genomes]
rs7233290	0.89[ASN][1000 genomes]
rs7235929	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7237135	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72875309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7504616	0.85[ASN][1000 genomes]
rs7505626	0.85[CHB][hapmap]
rs9944742	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9946108	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9950665	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9964041	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9964437	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9964720	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9966470	0.93[CHB][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3819091	TUBB6	cis	multi-tissue	Pritchard
rs3819091	MGC4083	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12326200-12366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr18:12333400-12366600	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
6	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
7	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
8	chr18:12333600-12366400	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr18:12333600-12369600	Strong transcription	Placenta	Placenta
10	chr18:12333600-12369800	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr18:12333800-12369400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr18:12334000-12369400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr18:12337000-12367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr18:12337000-12374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr18:12337200-12369400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:12337400-12369800	Strong transcription	Liver	Liver
17	chr18:12337400-12370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr18:12337800-12369600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr18:12337800-12370800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:12339200-12368800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr18:12339800-12370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr18:12339800-12371400	Strong transcription	Dnd41	blood
23	chr18:12340000-12365000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr18:12340000-12369400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr18:12340000-12369400	Strong transcription	HepG2	liver
26	chr18:12340000-12369600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr18:12340000-12370800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr18:12340000-12371400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr18:12340000-12371600	Strong transcription	GM12878-XiMat	blood
30	chr18:12340200-12366400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr18:12340200-12369400	Strong transcription	Hela-S3	cervix
32	chr18:12340400-12367400	Strong transcription	Thymus	Thymus
33	chr18:12341000-12370800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr18:12341000-12370800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr18:12341000-12370800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr18:12341600-12369400	Strong transcription	Lung	lung
37	chr18:12341600-12370800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr18:12341800-12369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr18:12349200-12369400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:12349600-12366000	Strong transcription	Fetal Intestine Small	intestine
41	chr18:12350600-12369600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr18:12353600-12369600	Strong transcription	Primary B cells from cord blood	blood
43	chr18:12354200-12369400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr18:12355200-12367600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr18:12355400-12367800	Strong transcription	HMEC	breast
46	chr18:12355400-12369400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr18:12356800-12369000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr18:12357800-12367800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr18:12357800-12369400	Strong transcription	Primary T cells from cord blood	blood
50	chr18:12357800-12369400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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