Variant report

Variant	rs11664282
Chromosome Location	chr18:12334409-12334410
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12304979..12308873-chr18:12332783..12336926,3	K562	blood:
2	chr18:12333793..12335382-chr18:12358022..12359784,2	K562	blood:
3	chr18:12334089..12335746-chr18:12343294..12345170,2	K562	blood:
4	chr18:12333547..12336346-chr18:12375267..12377221,2	K562	blood:
5	chr18:12334246..12336186-chr18:12342528..12345170,2	K562	blood:

Variant related genes	Relation type
ENSG00000141385	Chromatin interaction
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10853224	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11080567	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11267036	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11548177	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11659246	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11660106	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11660222	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11661684	0.80[ASN][1000 genomes]
rs11661708	0.80[ASN][1000 genomes]
rs11663340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11664255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12607250	0.83[EUR][1000 genomes]
rs12607321	0.80[ASN][1000 genomes]
rs12607378	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12960267	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12963761	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12965912	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35242253	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3819091	0.85[ASN][1000 genomes]
rs4796958	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4796959	0.80[ASN][1000 genomes]
rs4796960	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4796962	0.82[EUR][1000 genomes]
rs4796963	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4797673	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4797674	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4797675	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58136410	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6416994	0.80[ASN][1000 genomes]
rs6505749	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6505751	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7231304	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7233290	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7235929	0.80[ASN][1000 genomes]
rs7237135	0.83[ASN][1000 genomes]
rs7244254	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72875309	0.85[ASN][1000 genomes]
rs7504558	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7504575	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7504616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505208	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7505255	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7505626	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8083882	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8087843	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8098040	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8099636	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9303766	0.83[EUR][1000 genomes]
rs9303767	0.83[EUR][1000 genomes]
rs9303768	0.83[EUR][1000 genomes]
rs9652931	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9807444	0.83[EUR][1000 genomes]
rs9944742	0.80[ASN][1000 genomes]
rs9945901	0.82[EUR][1000 genomes]
rs9946108	0.80[ASN][1000 genomes]
rs9946172	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9946217	0.83[EUR][1000 genomes]
rs9946347	0.83[EUR][1000 genomes]
rs9949054	0.83[EUR][1000 genomes]
rs9950665	0.81[ASN][1000 genomes]
rs9958069	0.83[EUR][1000 genomes]
rs9958525	0.83[EUR][1000 genomes]
rs9964437	0.80[ASN][1000 genomes]
rs9964720	0.80[ASN][1000 genomes]
rs9966470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv3442047	chr18:12331977-12334525	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3408066	chr18:12332052-12334450	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11664282	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs11664282	TUBB6	cis	Whole Blood	GTEx
rs11664282	TUBB6	cis	multi-tissue	Pritchard
rs11664282	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL

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	chr18:12318400-12334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:12319000-12336800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr18:12320800-12348200	Strong transcription	Fetal Intestine Small	intestine
5	chr18:12323400-12342800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr18:12324800-12337000	Strong transcription	Liver	Liver
7	chr18:12324800-12338800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr18:12324800-12339400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr18:12325200-12335800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr18:12326000-12343200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr18:12326200-12366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:12328000-12335400	Weak transcription	Psoas Muscle	Psoas
13	chr18:12328000-12335600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr18:12328400-12334600	Weak transcription	Stomach Mucosa	stomach
15	chr18:12329600-12336800	Weak transcription	NHDF-Ad	bronchial
16	chr18:12331400-12334600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr18:12331400-12336800	Weak transcription	HUVEC	blood vessel
18	chr18:12333000-12336400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr18:12333000-12336800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr18:12333200-12336200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr18:12333200-12339600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr18:12333200-12362200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr18:12333400-12334600	Strong transcription	Pancreas	Pancrea
26	chr18:12333400-12334800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:12333400-12335600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:12333400-12335800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr18:12333400-12335800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr18:12333400-12336400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr18:12333400-12336400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr18:12333400-12337000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr18:12333400-12339000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr18:12333400-12339000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr18:12333400-12339000	Strong transcription	Colonic Mucosa	Colon
36	chr18:12333400-12339200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr18:12333400-12339600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr18:12333400-12339600	Strong transcription	Thymus	Thymus
39	chr18:12333400-12340800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr18:12333400-12366600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
42	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
43	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
44	chr18:12333600-12334600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr18:12333600-12334600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
46	chr18:12333600-12334600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
47	chr18:12333600-12334600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr18:12333600-12334800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr18:12333600-12334800	Strong transcription	NHEK	skin
50	chr18:12333600-12335000	Strong transcription	Gastric	stomach

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