Variant report

Variant	rs12960267
Chromosome Location	chr18:12312492-12312493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12312290..12313035-chr18:12320340..12321330,2	K562	blood:
2	chr18:12306891..12312604-chr18:12376208..12378768,5	K562	blood:
3	chr18:12311936..12317885-chr18:12323414..12329476,8	K562	blood:
4	chr18:12311231..12313531-chr18:12374709..12376964,3	K562	blood:

Variant related genes	Relation type
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10853224	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11080567	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11267036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11548177	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11659246	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11660106	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11660222	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11663340	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11664255	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11664282	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12455756	0.86[EUR][1000 genomes]
rs12607250	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12607321	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12607378	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12954560	0.84[EUR][1000 genomes]
rs12959653	0.83[ASN][1000 genomes]
rs12959674	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12960302	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs12963761	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12965912	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12970667	0.87[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs28625182	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34685983	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35242253	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3819091	0.85[CHB][hapmap]
rs4073975	0.82[YRI][hapmap]
rs4796958	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796959	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796960	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796962	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4797672	0.82[ASN][1000 genomes]
rs4797673	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4797674	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4797675	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58136410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61604633	0.87[EUR][1000 genomes]
rs62097556	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6505749	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505751	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7231304	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7233290	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7244254	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7244709	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7504558	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7504575	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7504616	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7505208	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7505255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083882	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8087843	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8098040	0.81[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8098700	0.82[ASN][1000 genomes]
rs8099636	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9303766	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9303767	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9303768	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9652931	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807444	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9945901	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9946172	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9946217	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9946347	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9949054	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9954945	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9958069	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9958525	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9964163	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9966470	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12960267	TUBB6	cis	multi-tissue	Pritchard
rs12960267	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs12960267	MGC4083	cis	multi-tissue	Pritchard
rs12960267	TUBB6	cis	Whole Blood	GTEx
rs12960267	TUBB6	cis	Lymphoblastoid	GTEx
rs12960267	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12309200-12316000	Weak transcription	Gastric	stomach
2	chr18:12309400-12312600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr18:12309600-12312800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:12309600-12317800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr18:12309800-12314200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:12309800-12315600	Weak transcription	Psoas Muscle	Psoas
7	chr18:12310000-12313000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:12310000-12313600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:12310000-12313600	Weak transcription	Aorta	Aorta
10	chr18:12310000-12315600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr18:12310000-12318000	Weak transcription	Esophagus	oesophagus
12	chr18:12310000-12318200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:12310000-12324800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:12310000-12325800	Weak transcription	Fetal Kidney	kidney
15	chr18:12310200-12312800	ZNF genes & repeats	K562	blood
16	chr18:12310200-12313400	Weak transcription	Pancreas	Pancrea
17	chr18:12310200-12313600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:12310200-12317600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr18:12310200-12319000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr18:12310200-12320400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr18:12310200-12324800	Weak transcription	HepG2	liver
22	chr18:12310400-12312600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr18:12310600-12312600	ZNF genes & repeats	A549	lung
24	chr18:12310600-12314600	Strong transcription	Ovary	ovary
25	chr18:12310600-12322800	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr18:12310800-12312600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
27	chr18:12310800-12312600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr18:12310800-12312600	ZNF genes & repeats	GM12878-XiMat	blood
29	chr18:12310800-12312800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr18:12310800-12312800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr18:12310800-12313000	Weak transcription	Fetal Heart	heart
32	chr18:12310800-12313400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr18:12311000-12312600	ZNF genes & repeats	NHDF-Ad	bronchial
34	chr18:12311000-12313000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr18:12311000-12313400	Strong transcription	NH-A	brain
36	chr18:12311000-12313800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr18:12311000-12313800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr18:12311000-12314200	Weak transcription	Right Ventricle	heart
39	chr18:12311000-12315600	Weak transcription	Lung	lung
40	chr18:12311000-12316200	Genic enhancers	HMEC	breast
41	chr18:12311000-12323200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr18:12311000-12324800	Weak transcription	Spleen	Spleen
43	chr18:12311200-12313400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:12311200-12314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr18:12311200-12314200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr18:12311200-12315400	Genic enhancers	HUVEC	blood vessel
47	chr18:12311200-12315600	Genic enhancers	HSMM	muscle
48	chr18:12311400-12312600	Strong transcription	Fetal Intestine Large	intestine
49	chr18:12311400-12312800	Strong transcription	Adipose Nuclei	Adipose
50	chr18:12311400-12313400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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