Variant report

Variant	rs2509510
Chromosome Location	chr18:12375613-12375614
allele	A/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:28974803..28975435-chr18:12375058..12375922,2	Hela-S3	cervix:
2	chr18:12361778..12363589-chr18:12374955..12376889,2	K562	blood:
3	chr18:12311231..12313531-chr18:12374709..12376964,3	K562	blood:
4	chr18:12305136..12307294-chr18:12373188..12375992,2	K562	blood:
5	chr18:12373675..12375792-chr18:12443379..12445132,2	K562	blood:
6	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
7	chr18:12358323..12362507-chr18:12375018..12379122,7	K562	blood:
8	chr18:12373949..12376848-chr18:12946851..12949234,5	K562	blood:
9	chr18:12375474..12376315-chr6:44214105..44215049,2	Hela-S3	cervix:
10	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
11	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
12	chr18:12375261..12378325-chr18:12405563..12409497,4	MCF-7	breast:
13	chr18:12375564..12378929-chr18:12655169..12659722,7	MCF-7	breast:
14	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
15	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
16	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:
17	chr18:12375309..12380137-chr18:12701387..12704274,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141391	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000176014	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10853225	0.84[AMR][1000 genomes]
rs11080571	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11080572	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11662523	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11664216	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11875938	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12455273	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12604732	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12954686	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12968566	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1547858	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1941222	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2003881	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298542	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298543	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28372882	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35968035	0.91[ASN][1000 genomes]
rs3786260	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478088	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797680	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs553091	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs566960	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs693449	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7231409	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7235237	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7235296	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7407640	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8097342	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9303771	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9635829	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9956171	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9960103	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9964406	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2509510	TUBB6	cis	Whole Blood	GTEx
rs2509510	SLMO1	cis	Thyroid	GTEx

Chromatin state (count:127 , 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	chr18:12369400-12375800	Weak transcription	NHLF	lung
5	chr18:12369400-12376000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr18:12370400-12375800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr18:12370800-12376000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr18:12371000-12375800	Enhancers	Thymus	Thymus
9	chr18:12371000-12376000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr18:12371000-12376000	Enhancers	Fetal Thymus	thymus
11	chr18:12371200-12376000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr18:12371400-12375800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr18:12371400-12376000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr18:12371400-12376000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr18:12371400-12376000	Enhancers	Stomach Mucosa	stomach
16	chr18:12371400-12376200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr18:12371800-12375800	Enhancers	Small Intestine	intestine
18	chr18:12372400-12375800	Enhancers	Liver	Liver
19	chr18:12372400-12375800	Enhancers	Ovary	ovary
20	chr18:12372400-12376000	Enhancers	Brain Hippocampus Middle	brain
21	chr18:12372600-12375800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr18:12372600-12376000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr18:12373000-12376000	Enhancers	Brain Angular Gyrus	brain
24	chr18:12373400-12376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr18:12373600-12375800	Weak transcription	NH-A	brain
26	chr18:12373800-12375800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr18:12373800-12375800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr18:12373800-12376400	Weak transcription	Aorta	Aorta
29	chr18:12374200-12375800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr18:12374200-12375800	Genic enhancers	Fetal Intestine Large	intestine
31	chr18:12374200-12376000	Enhancers	Primary T cells fromperipheralblood	blood
32	chr18:12374400-12375800	Weak transcription	Brain Germinal Matrix	brain
33	chr18:12374400-12376000	Enhancers	Brain Cingulate Gyrus	brain
34	chr18:12374400-12376200	Enhancers	Fetal Brain Male	brain
35	chr18:12374600-12375800	Weak transcription	Primary T cells from cord blood	blood
36	chr18:12374600-12375800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr18:12374600-12376000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr18:12374600-12376000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr18:12374600-12376000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr18:12374800-12375800	Weak transcription	Fetal Brain Female	brain
41	chr18:12374800-12375800	Weak transcription	Fetal Lung	lung
42	chr18:12374800-12375800	Enhancers	Fetal Muscle Trunk	muscle
43	chr18:12374800-12375800	Enhancers	Fetal Muscle Leg	muscle
44	chr18:12374800-12375800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr18:12374800-12376000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr18:12374800-12376000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:12374800-12376000	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr18:12374800-12376200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:12375000-12375800	Enhancers	Placenta	Placenta
50	chr18:12375000-12376000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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