Variant report

Variant	rs11663837
Chromosome Location	chr18:12376482-12376483
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:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:43833269..43834131-chr18:12376340..12377210,2	Hela-S3	cervix:
2	chr18:12361778..12363589-chr18:12374955..12376889,2	K562	blood:
3	chr18:12311231..12313531-chr18:12374709..12376964,3	K562	blood:
4	chr17:33307818..33308346-chr18:12376448..12377431,2	Hela-S3	cervix:
5	chr18:12306891..12312604-chr18:12376208..12378768,5	K562	blood:
6	chr18:12375314..12379217-chr18:12700733..12704866,11	K562	blood:
7	chr18:12358323..12362507-chr18:12375018..12379122,7	K562	blood:
8	chr18:12375743..12378274-chr18:12418543..12422031,3	MCF-7	breast:
9	chr18:12373949..12376848-chr18:12946851..12949234,5	K562	blood:
10	chr18:12376373..12377442-chr6:27100665..27101926,4	Hela-S3	cervix:
11	chr18:12375996..12378292-chr18:12406153..12409059,2	MCF-7	breast:
12	chr18:12306558..12308875-chr18:12376128..12379112,4	MCF-7	breast:
13	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
14	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
15	chr18:12375261..12378325-chr18:12405563..12409497,4	MCF-7	breast:
16	chr18:12375798..12379149-chr18:12946624..12949226,4	MCF-7	breast:
17	chr18:12375564..12378929-chr18:12655169..12659722,7	MCF-7	breast:
18	chr18:12376063..12377849-chr18:12702588..12704602,2	MCF-7	breast:
19	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
20	chr18:12375835..12378198-chr18:12677932..12680535,3	K562	blood:
21	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
22	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:
23	chr18:12307869..12309956-chr18:12375801..12377728,3	MCF-7	breast:
24	chr18:11979615..11982143-chr18:12376173..12378788,2	K562	blood:
25	chr18:12375309..12380137-chr18:12701387..12704274,11	K562	blood:
26	chr18:12375685..12377446-chr18:12655932..12658656,3	MCF-7	breast:
27	chr18:12375636..12378066-chr18:12991064..12992748,2	K562	blood:
28	chr16:771026..772819-chr18:12375664..12378170,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000141391	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000132141	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000176014	Chromatin interaction
ENSG00000066322	Chromatin interaction
ENSG00000103254	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12454398	1.00[ASW][hapmap]
rs35968035	0.85[ASN][1000 genomes]
rs3786260	0.80[CHD][hapmap]
rs478088	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs553091	0.83[ASN][1000 genomes]
rs566960	0.83[ASN][1000 genomes]
rs58955847	0.90[ASN][1000 genomes]
rs693449	0.83[ASN][1000 genomes]
rs7505859	1.00[ASW][hapmap]
rs9303770	0.80[CHD][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11663837	TUBB6	cis	lymphoblastoid	seeQTL
rs11663837	ANKRD30B	cis	cerebellum	SCAN
rs11663837	SPIRE1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12375000-12378000	Active TSS	HSMM	muscle
2	chr18:12375200-12376600	Flanking Active TSS	Dnd41	blood
3	chr18:12375200-12376800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr18:12375200-12376800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr18:12375200-12378200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr18:12375200-12378400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr18:12375200-12378400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr18:12375200-12378400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr18:12375400-12376600	Flanking Active TSS	Pancreas	Pancrea
10	chr18:12375400-12377000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr18:12375400-12377000	Active TSS	Fetal Heart	heart
12	chr18:12375400-12377200	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr18:12375400-12377800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr18:12375400-12378200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr18:12375400-12378400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr18:12375400-12378400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr18:12375400-12378600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:12375600-12376600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr18:12375600-12376800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr18:12375600-12377800	Active TSS	Muscle Satellite Cultured Cells	--
21	chr18:12375600-12378000	Active TSS	Hela-S3	cervix
22	chr18:12375600-12378200	Active TSS	Left Ventricle	heart
23	chr18:12375600-12378200	Active TSS	A549	lung
24	chr18:12375600-12378400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr18:12375600-12378600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr18:12375800-12376600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr18:12375800-12376600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:12375800-12376600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr18:12375800-12376600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:12375800-12376600	Flanking Active TSS	Liver	Liver
31	chr18:12375800-12376600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr18:12375800-12376600	Flanking Active TSS	Fetal Brain Female	brain
33	chr18:12375800-12376600	Flanking Active TSS	Placenta	Placenta
34	chr18:12375800-12376800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr18:12375800-12376800	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr18:12375800-12376800	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr18:12375800-12376800	Flanking Active TSS	NH-A	brain
38	chr18:12375800-12377200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:12375800-12377800	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr18:12375800-12378000	Active TSS	Gastric	stomach
41	chr18:12375800-12378400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr18:12375800-12378600	Active TSS	HMEC	breast
43	chr18:12376000-12376600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr18:12376000-12376600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr18:12376000-12376600	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr18:12376000-12376600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr18:12376000-12376600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr18:12376000-12376600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr18:12376000-12376600	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr18:12376000-12376600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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