Variant report

Variant	rs9303770
Chromosome Location	chr18:12369341-12369342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10853225	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11080564	0.83[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.82[YRI][hapmap]
rs11080571	0.83[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11080572	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129115	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs11553521	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11662523	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11663837	0.80[CHD][hapmap]
rs11664216	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11875938	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12455273	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12456857	0.83[ASW][hapmap];0.80[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs12604732	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954686	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12968089	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12968566	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1547858	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941222	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003881	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298542	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298543	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2509510	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28372882	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35968035	0.91[ASN][1000 genomes]
rs3786260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478088	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4797677	0.80[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4797680	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553091	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs566960	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs693449	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7231182	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231409	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7235237	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7235296	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7407640	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7504908	0.85[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs7504974	0.85[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs7505834	0.80[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap]
rs8086993	0.83[ASW][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap]
rs8092506	0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs8093375	0.95[CEU][hapmap]
rs8097342	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303769	0.85[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9303771	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9635829	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9956171	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9960103	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9964406	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9303770	TUBB6	cis	Whole Blood	GTEx
rs9303770	MEST	trans	lymphoblastoid	seeQTL
rs9303770	TUBB6	cis	multi-tissue	Pritchard
rs9303770	TUBB6	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
2	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
4	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
5	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
6	chr18:12333600-12369600	Strong transcription	Placenta	Placenta
7	chr18:12333600-12369800	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr18:12333800-12369400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr18:12334000-12369400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr18:12337000-12374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr18:12337200-12369400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:12337400-12369800	Strong transcription	Liver	Liver
13	chr18:12337400-12370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr18:12337800-12369600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr18:12337800-12370800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:12339800-12370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr18:12339800-12371400	Strong transcription	Dnd41	blood
18	chr18:12340000-12369400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:12340000-12369400	Strong transcription	HepG2	liver
20	chr18:12340000-12369600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr18:12340000-12370800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr18:12340000-12371400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:12340000-12371600	Strong transcription	GM12878-XiMat	blood
24	chr18:12340200-12369400	Strong transcription	Hela-S3	cervix
25	chr18:12341000-12370800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr18:12341000-12370800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr18:12341000-12370800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr18:12341600-12369400	Strong transcription	Lung	lung
29	chr18:12341600-12370800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr18:12341800-12369400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr18:12349200-12369400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr18:12350600-12369600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr18:12353600-12369600	Strong transcription	Primary B cells from cord blood	blood
34	chr18:12354200-12369400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr18:12355400-12369400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr18:12357800-12369400	Strong transcription	Primary T cells from cord blood	blood
37	chr18:12357800-12369400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr18:12357800-12369600	Strong transcription	Esophagus	oesophagus
39	chr18:12358000-12372400	Strong transcription	NHEK	skin
40	chr18:12358200-12369400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr18:12358200-12369600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr18:12358600-12371400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr18:12359200-12370800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr18:12359200-12376000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr18:12359800-12375800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr18:12360000-12373400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr18:12360600-12369400	Strong transcription	Fetal Brain Female	brain
48	chr18:12361400-12369400	Strong transcription	Brain Germinal Matrix	brain
49	chr18:12361800-12369600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr18:12362200-12369400	Strong transcription	Muscle Satellite Cultured Cells	--

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