Variant report

Variant	rs12373207
Chromosome Location	chr18:12725236-12725237
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1062235	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1129214	0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12373259	0.88[ASN][1000 genomes]
rs12454322	0.81[EUR][1000 genomes]
rs12455268	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12455295	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12457026	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12457771	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12458097	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12458895	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12954079	0.90[ASN][1000 genomes]
rs12957555	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12957603	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12957810	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12960623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12960997	0.90[ASN][1000 genomes]
rs12962598	0.90[ASN][1000 genomes]
rs12963505	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12964507	0.89[ASN][1000 genomes]
rs12965733	0.84[ASN][1000 genomes]
rs12965990	0.90[ASN][1000 genomes]
rs12966246	0.84[ASN][1000 genomes]
rs12966367	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12966424	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12968771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12969300	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12969446	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12969938	0.90[ASN][1000 genomes]
rs12971256	0.84[ASN][1000 genomes]
rs1362709	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1549011	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1592642	0.84[ASN][1000 genomes]
rs1592643	0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs17616402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1971702	0.84[ASN][1000 genomes]
rs2011575	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2011579	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051262	0.89[ASN][1000 genomes]
rs2302768	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs28820339	0.85[ASN][1000 genomes]
rs28832066	0.90[ASN][1000 genomes]
rs34040888	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34120824	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34277169	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34472716	0.82[ASN][1000 genomes]
rs34537593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34632667	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34690304	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34847769	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35322088	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35506854	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35634465	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35699948	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35898717	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809919	0.89[ASN][1000 genomes]
rs3902981	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4296322	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs45589535	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45596833	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4633785	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs55870255	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62095975	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096023	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62096046	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62096048	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6505760	0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs66808227	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7229168	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs7233175	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7233694	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7507018	0.90[ASN][1000 genomes]
rs8083182	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8086099	0.84[ASN][1000 genomes]
rs8086265	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8086846	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8097134	0.84[ASN][1000 genomes]
rs9303774	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303775	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9303776	0.88[ASN][1000 genomes]
rs933600	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs948319	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs963920	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9945140	0.90[ASN][1000 genomes]
rs9945644	0.90[ASN][1000 genomes]
rs9945801	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9948844	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9949293	0.90[ASN][1000 genomes]
rs9950365	0.90[ASN][1000 genomes]
rs9951576	0.90[ASN][1000 genomes]
rs9952000	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9954112	0.90[ASN][1000 genomes]
rs9955985	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9957880	0.89[ASN][1000 genomes]
rs9958100	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs9958412	0.90[ASN][1000 genomes]
rs9959039	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9959458	0.90[ASN][1000 genomes]
rs9959536	0.89[ASN][1000 genomes]
rs9960555	0.89[ASN][1000 genomes]
rs9961799	0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs9962006	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9963809	0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs9964868	0.93[ASN][1000 genomes]
rs9966464	0.89[ASN][1000 genomes]
rs9966490	0.91[ASN][1000 genomes]
rs9966672	0.91[ASN][1000 genomes]
rs9967437	0.90[ASN][1000 genomes]
rs9967553	0.91[ASN][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	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	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12373207	SPIRE1	cis	Muscle Skeletal	GTEx
rs12373207	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs12373207	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12704200-12726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:12704800-12727200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:12704800-12727800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:12705000-12728600	Weak transcription	Stomach Mucosa	stomach
5	chr18:12705400-12726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr18:12705400-12727200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:12705600-12726000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr18:12705600-12727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr18:12705600-12727200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr18:12705600-12727200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr18:12705600-12727200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr18:12705800-12726600	Strong transcription	Fetal Thymus	thymus
13	chr18:12705800-12727000	Strong transcription	Placenta	Placenta
14	chr18:12705800-12727200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr18:12705800-12727200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr18:12705800-12727200	Strong transcription	Fetal Muscle Leg	muscle
17	chr18:12706000-12727000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:12706000-12727200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:12706200-12726000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr18:12706200-12726800	Strong transcription	Fetal Intestine Large	intestine
21	chr18:12706200-12727200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr18:12706200-12727200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr18:12706400-12726600	Strong transcription	Liver	Liver
24	chr18:12706400-12727000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr18:12706400-12727000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr18:12706400-12727200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr18:12706600-12727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr18:12706600-12727200	Strong transcription	Adipose Nuclei	Adipose
29	chr18:12706800-12727000	Strong transcription	Dnd41	blood
30	chr18:12708600-12726800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr18:12709200-12725600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr18:12709200-12726200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:12709200-12726800	Strong transcription	Osteobl	bone
34	chr18:12709600-12725800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr18:12709600-12726400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr18:12710200-12727000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr18:12710200-12727200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr18:12710200-12727200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr18:12712600-12727000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr18:12712800-12725400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr18:12712800-12727200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr18:12713600-12725600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr18:12713600-12726200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr18:12713800-12726000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr18:12713800-12726800	Weak transcription	Fetal Brain Male	brain
46	chr18:12714400-12726600	Weak transcription	Brain Substantia Nigra	brain
47	chr18:12714400-12726800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr18:12714600-12728800	Weak transcription	Esophagus	oesophagus
49	chr18:12715400-12725800	Weak transcription	Pancreas	Pancrea
50	chr18:12715600-12727000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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