Variant report

Variant	rs2003881
Chromosome Location	chr18:12374923-12374924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12311231..12313531-chr18:12374709..12376964,3	K562	blood:
2	chr18:12305136..12307294-chr18:12373188..12375992,2	K562	blood:
3	chr18:12354405..12356233-chr18:12373233..12375178,2	K562	blood:
4	chr18:12373675..12375792-chr18:12443379..12445132,2	K562	blood:
5	chr18:12373949..12376848-chr18:12946851..12949234,5	K562	blood:
6	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
7	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
8	chr18:12352685..12355355-chr18:12373125..12375280,2	MCF-7	breast:
9	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
10	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
11	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000176014	Chromatin interaction
ENSG00000141391	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10853225	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11080571	0.83[EUR][1000 genomes]
rs11080572	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11553521	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11662523	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11664216	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11875938	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12455273	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12604732	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12968089	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12968566	0.83[EUR][1000 genomes]
rs1547858	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1941222	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298542	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298543	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2509510	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28372882	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35968035	0.87[ASN][1000 genomes]
rs3786260	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs478088	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797677	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4797680	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553091	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs566960	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs693449	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7231182	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7231409	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7235237	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7235296	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7407640	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8097342	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9303769	0.85[EUR][1000 genomes]
rs9303771	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9635829	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9956171	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9960103	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9964406	0.89[AMR][1000 genomes];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2003881	TUBB6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12359200-12376000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:12359800-12375800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr18:12367600-12376000	Weak transcription	Fetal Kidney	kidney
4	chr18:12367800-12375400	Weak transcription	HMEC	breast
5	chr18:12368800-12375400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:12369400-12375000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr18:12369400-12375000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr18:12369400-12375400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr18:12369400-12375600	Weak transcription	A549	lung
10	chr18:12369400-12375800	Weak transcription	NHLF	lung
11	chr18:12369400-12376000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr18:12369600-12375000	Weak transcription	Placenta	Placenta
13	chr18:12369600-12375000	Weak transcription	Spleen	Spleen
14	chr18:12369600-12375200	Weak transcription	Primary B cells from cord blood	blood
15	chr18:12369600-12375400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr18:12369600-12375400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr18:12369600-12375400	Weak transcription	Esophagus	oesophagus
18	chr18:12370000-12375200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr18:12370400-12375800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr18:12370800-12375400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr18:12370800-12376000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr18:12371000-12375800	Enhancers	Thymus	Thymus
23	chr18:12371000-12376000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr18:12371000-12376000	Enhancers	Fetal Thymus	thymus
25	chr18:12371200-12376000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr18:12371400-12375800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr18:12371400-12376000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr18:12371400-12376000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr18:12371400-12376000	Enhancers	Stomach Mucosa	stomach
30	chr18:12371400-12376200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr18:12371600-12375200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr18:12371800-12375000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr18:12371800-12375800	Enhancers	Small Intestine	intestine
34	chr18:12372000-12375200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr18:12372000-12375400	Enhancers	Pancreas	Pancrea
36	chr18:12372400-12375000	Enhancers	Brain Substantia Nigra	brain
37	chr18:12372400-12375000	Genic enhancers	NHEK	skin
38	chr18:12372400-12375800	Enhancers	Liver	Liver
39	chr18:12372400-12375800	Enhancers	Ovary	ovary
40	chr18:12372400-12376000	Enhancers	Brain Hippocampus Middle	brain
41	chr18:12372600-12375200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr18:12372600-12375800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr18:12372600-12376000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr18:12373000-12375400	Weak transcription	NHDF-Ad	bronchial
45	chr18:12373000-12376000	Enhancers	Brain Angular Gyrus	brain
46	chr18:12373200-12375400	Strong transcription	Fetal Stomach	stomach
47	chr18:12373400-12375000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr18:12373400-12375200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:12373400-12375200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr18:12373400-12375400	Enhancers	HUES6 Cell Line	embryonic stem cell

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