Variant report

Variant	rs17616124
Chromosome Location	chr18:12596780-12596781
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12595958..12597985-chr18:12607168..12608800,2	MCF-7	breast:
2	chr18:12596375..12597992-chr18:12655323..12658248,2	MCF-7	breast:
3	chr18:12594070..12599084-chr18:12599553..12605396,7	K562	blood:
4	chr18:12590720..12592550-chr18:12594454..12597445,2	MCF-7	breast:
5	chr18:12595174..12598244-chr18:12625042..12627627,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1105748	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954606	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955162	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955176	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12959459	1.00[ASN][1000 genomes]
rs12959998	1.00[ASN][1000 genomes]
rs12961307	1.00[ASN][1000 genomes]
rs12961711	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971000	1.00[ASN][1000 genomes]
rs17524639	1.00[ASN][1000 genomes]
rs17525318	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525459	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615525	1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34215298	1.00[ASN][1000 genomes]
rs34229934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34371240	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34460164	1.00[ASN][1000 genomes]
rs34469203	1.00[ASN][1000 genomes]
rs34503700	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34512782	1.00[ASN][1000 genomes]
rs34737110	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34859829	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34933611	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35082337	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35309605	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35532404	1.00[ASN][1000 genomes]
rs35612342	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	1.00[ASN][1000 genomes]
rs35643117	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35686128	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351482	1.00[ASN][1000 genomes]
rs71351484	1.00[ASN][1000 genomes]
rs71351485	1.00[ASN][1000 genomes]
rs71351491	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351495	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	1.00[ASN][1000 genomes]
rs71363149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17616124	SLMO1	cis	Artery Tibial	GTEx
rs17616124	RP11-861E21.1	cis	Artery Tibial	GTEx
rs17616124	AP001029.1	cis	Artery Tibial	GTEx
rs17616124	RP11-861E21.2	cis	Thyroid	GTEx
rs17616124	SPIRE1	cis	Thyroid	GTEx
rs17616124	SPIRE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12587800-12596800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr18:12589600-12597000	Weak transcription	Aorta	Aorta
3	chr18:12589800-12597200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr18:12589800-12597200	Weak transcription	Ovary	ovary
5	chr18:12589800-12597400	Weak transcription	Brain Angular Gyrus	brain
6	chr18:12590000-12597400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr18:12590800-12597200	Weak transcription	Fetal Brain Male	brain
8	chr18:12590800-12597800	Weak transcription	Pancreas	Pancrea
9	chr18:12590800-12599200	Weak transcription	Liver	Liver
10	chr18:12591200-12596800	Weak transcription	Fetal Brain Female	brain
11	chr18:12591400-12596800	Weak transcription	Left Ventricle	heart
12	chr18:12591400-12596800	Weak transcription	Right Atrium	heart
13	chr18:12592400-12597600	Weak transcription	Colon Smooth Muscle	Colon
14	chr18:12592800-12597800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:12593000-12596800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:12594200-12597600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:12594400-12596800	Weak transcription	Osteobl	bone
18	chr18:12594600-12600400	Enhancers	HepG2	liver
19	chr18:12595400-12596800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr18:12595400-12597000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr18:12595400-12597000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr18:12595400-12597200	Enhancers	HSMMtube	muscle
23	chr18:12595400-12598200	Enhancers	Brain Anterior Caudate	brain
24	chr18:12595400-12599400	Enhancers	Fetal Heart	heart
25	chr18:12595400-12600400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr18:12595600-12596800	Enhancers	Primary T cells from cord blood	blood
27	chr18:12595600-12597200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr18:12595600-12597200	Enhancers	HSMM	muscle
29	chr18:12595600-12597600	Enhancers	HUVEC	blood vessel
30	chr18:12595600-12598000	Enhancers	Brain Substantia Nigra	brain
31	chr18:12595600-12600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr18:12595600-12600400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr18:12595600-12600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr18:12595800-12598200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:12595800-12599000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr18:12595800-12600600	Enhancers	HMEC	breast
37	chr18:12596000-12597000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr18:12596000-12597000	Enhancers	K562	blood
39	chr18:12596000-12597400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr18:12596000-12597600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr18:12596000-12598000	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr18:12596000-12599200	Enhancers	Fetal Lung	lung
43	chr18:12596000-12599600	Enhancers	Fetal Kidney	kidney
44	chr18:12596200-12597000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr18:12596200-12597400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr18:12596200-12597400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr18:12596200-12599200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:12596400-12596800	Weak transcription	Brain Hippocampus Middle	brain
49	chr18:12596400-12596800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr18:12596400-12597000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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