Variant report

Variant	rs8086846
Chromosome Location	chr18:12642006-12642007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12639720..12643637-chr18:12655833..12659154,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000215527	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12373207	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12454322	0.82[EUR][1000 genomes]
rs12455268	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12455295	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12457771	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12458097	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12458895	0.85[EUR][1000 genomes]
rs12957555	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12957603	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12957810	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12963505	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12966367	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12969300	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17616402	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2011575	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2011579	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34040888	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34120824	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34277169	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34472716	0.81[ASN][1000 genomes]
rs34537593	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34632667	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34690304	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34847769	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35322088	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35506854	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35634465	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35699948	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35898717	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs45589535	0.86[EUR][1000 genomes]
rs45596833	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55870255	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62095975	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62096023	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62096046	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62096048	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66808227	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7233175	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7233694	0.87[EUR][1000 genomes]
rs8083182	0.86[EUR][1000 genomes]
rs8086265	0.85[EUR][1000 genomes]
rs9303774	0.89[EUR][1000 genomes]
rs933600	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs963920	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9948844	0.84[EUR][1000 genomes]
rs9959039	0.87[EUR][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	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv3428398	chr18:12641796-12642018	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8086846	SPIRE1	cis	Muscle Skeletal	GTEx
rs8086846	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs8086846	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12607800-12651800	Weak transcription	Brain Germinal Matrix	brain
2	chr18:12616400-12644800	Weak transcription	Brain Hippocampus Middle	brain
3	chr18:12616600-12645200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12621200-12645200	Weak transcription	Fetal Muscle Leg	muscle
5	chr18:12622800-12645000	Weak transcription	Brain Angular Gyrus	brain
6	chr18:12630400-12645400	Weak transcription	Ovary	ovary
7	chr18:12631000-12645200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:12631000-12645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr18:12631200-12647800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr18:12631400-12645200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
12	chr18:12635000-12645800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr18:12635200-12645800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:12637800-12643400	Weak transcription	Psoas Muscle	Psoas
15	chr18:12637800-12645400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:12637800-12652000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr18:12638400-12642200	Weak transcription	Left Ventricle	heart
18	chr18:12638600-12643200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr18:12638800-12645000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr18:12638800-12645200	Weak transcription	Brain Anterior Caudate	brain
21	chr18:12639000-12644800	Weak transcription	Fetal Brain Female	brain
22	chr18:12639000-12645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr18:12639600-12645800	Weak transcription	Esophagus	oesophagus
24	chr18:12640400-12652000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr18:12640800-12642200	Weak transcription	Liver	Liver
26	chr18:12640800-12642600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:12640800-12643200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr18:12640800-12645000	Weak transcription	Brain Substantia Nigra	brain
29	chr18:12641000-12642400	Weak transcription	Fetal Heart	heart
30	chr18:12641000-12642600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr18:12641000-12642600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr18:12641000-12644000	Weak transcription	Fetal Brain Male	brain
33	chr18:12641000-12644800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr18:12641000-12645200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr18:12641000-12645200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr18:12641000-12645200	Weak transcription	Pancreas	Pancrea
37	chr18:12641000-12645400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr18:12641000-12645400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr18:12641000-12645800	Weak transcription	K562	blood
40	chr18:12641000-12646000	Weak transcription	Right Ventricle	heart
41	chr18:12641000-12648200	Weak transcription	Hela-S3	cervix
42	chr18:12641200-12642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr18:12641200-12642200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr18:12641200-12642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr18:12641200-12642600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:12641200-12642600	Weak transcription	Colon Smooth Muscle	Colon
47	chr18:12641200-12643200	Weak transcription	HSMMtube	muscle
48	chr18:12641200-12643400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr18:12641200-12643400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:12641200-12643400	Weak transcription	A549	lung

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