Variant report

Variant	rs12970939
Chromosome Location	chr18:12654192-12654193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr18:12654183-12654380	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12648702..12654959-chr18:12655130..12658770,8	K562	blood:
2	chr18:12543497..12545408-chr18:12653876..12656459,2	MCF-7	breast:
3	chr18:12643422..12646156-chr18:12653146..12655533,3	MCF-7	breast:
4	chr18:12649857..12654959-chr18:12655130..12658770,11	K562	blood:

Variant related genes	Relation type
ENSG00000215527	TF binding region
PSMG2	TF binding region
SPIRE1	TF binding region
ENSG00000128789	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1105748	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954606	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955162	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12955176	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12956026	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[ASN][1000 genomes]
rs12961307	1.00[ASN][1000 genomes]
rs12961711	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12971000	1.00[ASN][1000 genomes]
rs17524639	1.00[ASN][1000 genomes]
rs17525318	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525459	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615525	1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17616124	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34215298	1.00[ASN][1000 genomes]
rs34229934	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34371240	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34460164	1.00[ASN][1000 genomes]
rs34469203	1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34512782	1.00[ASN][1000 genomes]
rs34737110	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34859829	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34933611	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35082337	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35309605	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35643117	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35686128	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	0.90[AFR][1000 genomes];0.88[AMR][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	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351495	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71363149	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3397790	chr18:12649001-12673755	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv576497	chr18:12650900-12658293	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv576498	chr18:12650900-12658436	Weak transcription Enhancers Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12970939	SLMO1	cis	Artery Tibial	GTEx
rs12970939	AP001029.1	cis	Artery Tibial	GTEx
rs12970939	RP11-861E21.1	cis	Artery Tibial	GTEx
rs12970939	SPIRE1	cis	Thyroid	GTEx
rs12970939	RP11-861E21.2	cis	Thyroid	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
2	chr18:12646200-12657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:12646200-12657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:12646400-12656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr18:12646400-12656600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr18:12646400-12657000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:12648000-12656800	Weak transcription	Left Ventricle	heart
8	chr18:12648400-12656600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:12648600-12655800	Weak transcription	Fetal Muscle Leg	muscle
10	chr18:12648600-12656800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr18:12650000-12654400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr18:12652200-12655400	Enhancers	Fetal Brain Male	brain
13	chr18:12652600-12655400	Weak transcription	Fetal Kidney	kidney
14	chr18:12652800-12654200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr18:12653000-12655800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr18:12653200-12656400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr18:12653200-12656600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr18:12653200-12656600	Weak transcription	Right Atrium	heart
19	chr18:12653200-12656600	Weak transcription	Right Ventricle	heart
20	chr18:12653200-12656800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:12653200-12656800	Weak transcription	Esophagus	oesophagus
22	chr18:12653200-12657000	Weak transcription	Spleen	Spleen
23	chr18:12653400-12654200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr18:12653400-12655000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr18:12653400-12655000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr18:12653400-12655400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr18:12653400-12655400	Weak transcription	NHEK	skin
28	chr18:12653400-12655600	Weak transcription	HMEC	breast
29	chr18:12653400-12656400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr18:12653400-12656400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr18:12653400-12656600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr18:12653400-12656600	Weak transcription	Aorta	Aorta
33	chr18:12653400-12656600	Weak transcription	Psoas Muscle	Psoas
34	chr18:12653400-12657000	Weak transcription	Pancreas	Pancrea
35	chr18:12653400-12657000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr18:12653600-12655000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr18:12653600-12655000	Active TSS	Fetal Brain Female	brain
38	chr18:12653600-12655200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:12653600-12655200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr18:12653600-12655400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:12653600-12655400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr18:12653600-12655400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr18:12653600-12655400	Weak transcription	Brain Angular Gyrus	brain
44	chr18:12653600-12655400	Weak transcription	Brain Anterior Caudate	brain
45	chr18:12653600-12655400	Weak transcription	Brain Germinal Matrix	brain
46	chr18:12653600-12655400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr18:12653600-12655400	Weak transcription	Brain Substantia Nigra	brain
48	chr18:12653600-12655400	Weak transcription	Fetal Heart	heart
49	chr18:12653600-12655400	Weak transcription	HSMMtube	muscle
50	chr18:12653600-12655400	Weak transcription	NH-A	brain

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