Variant report

Variant	rs12957885
Chromosome Location	chr18:12516219-12516220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs35508931	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35643817	1.00[AFR][1000 genomes]
rs61750780	1.00[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	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
5	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
6	nsv2208	chr18:12472999-12518189	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	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
8	esv2756075	chr18:12481377-12548970	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12957885	SPIRE1	Cis_1M	lymphoblastoid	RTeQTL
rs12957885	SLMO1	cis	Thyroid	GTEx
rs12957885	SLMO1	cis	Artery Tibial	GTEx
rs12957885	AP001029.1	cis	Esophagus Muscularis	GTEx
rs12957885	SLMO1	cis	Esophagus Muscularis	GTEx
rs12957885	AP001029.1	cis	Thyroid	GTEx
rs12957885	SLMO1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12460200-12516600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
3	chr18:12492200-12530400	Weak transcription	HepG2	liver
4	chr18:12492200-12532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr18:12492200-12548600	Weak transcription	Fetal Kidney	kidney
6	chr18:12493000-12541200	Weak transcription	NHEK	skin
7	chr18:12493200-12518400	Weak transcription	Esophagus	oesophagus
8	chr18:12493200-12520000	Weak transcription	Colon Smooth Muscle	Colon
9	chr18:12493200-12520400	Weak transcription	Psoas Muscle	Psoas
10	chr18:12493200-12551800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr18:12497600-12518000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:12500800-12520600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:12502000-12520600	Weak transcription	Fetal Stomach	stomach
14	chr18:12505200-12536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr18:12505400-12529400	Weak transcription	HMEC	breast
16	chr18:12505600-12520000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr18:12507000-12516400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr18:12507000-12526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr18:12507400-12535200	Weak transcription	Fetal Muscle Leg	muscle
20	chr18:12507800-12518000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr18:12509400-12539200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr18:12511400-12520000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr18:12511400-12520200	Weak transcription	HSMM	muscle
24	chr18:12511400-12521600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:12511400-12551800	Weak transcription	Lung	lung
26	chr18:12511800-12520400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr18:12511800-12520600	Weak transcription	HSMMtube	muscle
28	chr18:12512200-12518000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:12514400-12518200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr18:12514600-12522000	Enhancers	Fetal Brain Male	brain
31	chr18:12514800-12516400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr18:12515000-12516600	Enhancers	Fetal Lung	lung
33	chr18:12515000-12516800	Enhancers	HUVEC	blood vessel
34	chr18:12515200-12516800	Enhancers	Adipose Nuclei	Adipose
35	chr18:12515400-12516600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr18:12515400-12517600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr18:12515600-12516400	Enhancers	Right Atrium	heart
38	chr18:12515600-12516600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr18:12515600-12516600	Enhancers	Left Ventricle	heart
40	chr18:12515600-12516800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr18:12515600-12516800	Enhancers	Brain Cingulate Gyrus	brain
42	chr18:12515600-12516800	Flanking Active TSS	Fetal Brain Female	brain
43	chr18:12515600-12516800	Enhancers	Osteobl	bone
44	chr18:12515600-12517000	Enhancers	K562	blood
45	chr18:12515600-12517800	Enhancers	Brain Anterior Caudate	brain
46	chr18:12515600-12521400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr18:12515800-12516400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr18:12515800-12516400	Enhancers	Placenta	Placenta
49	chr18:12515800-12517000	Enhancers	Brain Hippocampus Middle	brain
50	chr18:12515800-12517000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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