Variant report

Variant	rs8092506
Chromosome Location	chr18:12321605-12321606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12320304..12322638-chr18:12766672..12769392,2	K562	blood:
2	chr18:12321262..12324555-chr18:12324806..12328664,5	K562	blood:
3	chr18:12320474..12322943-chr18:12328685..12331399,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10459999	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10460000	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10460001	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10853225	0.82[EUR][1000 genomes]
rs11080564	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080565	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080569	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11080571	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080572	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1129115	0.95[CEU][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11553521	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11662523	0.95[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11664216	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11665134	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11875938	0.86[EUR][1000 genomes]
rs12455273	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12455770	0.84[EUR][1000 genomes]
rs12456857	1.00[CEU][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12604732	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12954686	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12968089	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12968566	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1941222	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs2298542	0.80[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs2298543	0.80[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs28372882	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34314823	0.83[EUR][1000 genomes]
rs34829762	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35338639	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3786260	0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs478088	0.80[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs4796961	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4796964	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4797677	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4797680	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs62098961	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7231182	0.95[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7231409	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7235237	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7235296	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7407640	0.95[CEU][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs7504908	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7504974	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7505834	1.00[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8086821	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8086993	0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8087840	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8097342	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9303769	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9303770	0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs9946698	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9951945	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9956171	0.80[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8092506	TUBB6	cis	lymphoblastoid	seeQTL
rs8092506	TUBB6	cis	Lymphoblastoid	GTEx
rs8092506	MEST	trans	lymphoblastoid	seeQTL
rs8092506	TUBB6	cis	Whole Blood	GTEx
rs8092506	TUBB6	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12310000-12324800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:12310000-12325800	Weak transcription	Fetal Kidney	kidney
3	chr18:12310200-12324800	Weak transcription	HepG2	liver
4	chr18:12310600-12322800	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr18:12311000-12323200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:12311000-12324800	Weak transcription	Spleen	Spleen
7	chr18:12312600-12325000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr18:12312600-12332600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:12312800-12324800	Weak transcription	Colonic Mucosa	Colon
10	chr18:12312800-12324800	Weak transcription	Fetal Brain Female	brain
11	chr18:12314000-12333600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr18:12314200-12323000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr18:12314200-12327800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr18:12314400-12342600	Weak transcription	Small Intestine	intestine
15	chr18:12314600-12324400	Weak transcription	Brain Germinal Matrix	brain
16	chr18:12315600-12324800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr18:12316200-12324600	Weak transcription	Gastric	stomach
18	chr18:12316200-12325000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr18:12316400-12323000	Weak transcription	Fetal Lung	lung
20	chr18:12316400-12333600	Weak transcription	Fetal Brain Male	brain
21	chr18:12316600-12324400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:12316600-12324800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr18:12316600-12327000	Weak transcription	Stomach Mucosa	stomach
24	chr18:12316800-12327600	Strong transcription	HUVEC	blood vessel
25	chr18:12317600-12324800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr18:12317800-12322200	Strong transcription	NH-A	brain
27	chr18:12318000-12325000	Weak transcription	Hela-S3	cervix
28	chr18:12318000-12331200	Strong transcription	HMEC	breast
29	chr18:12318400-12324800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr18:12318400-12334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:12318600-12324400	Weak transcription	Thymus	Thymus
32	chr18:12318600-12324800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:12318600-12324800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr18:12318600-12324800	Weak transcription	Aorta	Aorta
35	chr18:12318600-12324800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr18:12318600-12325200	Weak transcription	Psoas Muscle	Psoas
37	chr18:12318600-12331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr18:12318800-12323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr18:12318800-12324800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:12318800-12324800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr18:12318800-12324800	Strong transcription	Fetal Stomach	stomach
42	chr18:12318800-12325000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr18:12318800-12327200	Weak transcription	Right Atrium	heart
44	chr18:12318800-12327600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr18:12319000-12333800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr18:12319000-12336800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr18:12319400-12323600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr18:12319600-12325400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr18:12320000-12324800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr18:12320200-12322000	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links