Variant report

Variant	rs9945374
Chromosome Location	chr18:12619841-12619842
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	chr18:12610305..12612983-chr18:12619196..12621821,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12454322	0.84[AFR][1000 genomes]
rs12454931	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12455093	0.81[EUR][1000 genomes]
rs12455909	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12604400	0.86[EUR][1000 genomes]
rs12604541	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12605240	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12606465	0.82[ASN][1000 genomes]
rs12606482	0.83[ASN][1000 genomes]
rs12606506	0.91[EUR][1000 genomes]
rs12954614	0.86[EUR][1000 genomes]
rs12958200	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12959015	0.91[EUR][1000 genomes]
rs12962476	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12965094	0.91[EUR][1000 genomes]
rs12970025	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12970174	0.83[EUR][1000 genomes]
rs1940974	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28414067	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28457089	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28582228	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28647784	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28886423	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34072260	0.92[EUR][1000 genomes]
rs34438212	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34814556	0.90[EUR][1000 genomes]
rs34899007	0.91[EUR][1000 genomes]
rs35449211	0.90[EUR][1000 genomes]
rs35630805	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4389196	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4493131	0.82[EUR][1000 genomes]
rs62097102	0.82[EUR][1000 genomes]
rs62097126	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62097148	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62097149	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62097153	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67045810	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7238546	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7242395	0.90[EUR][1000 genomes]
rs8088786	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8089081	0.88[EUR][1000 genomes]
rs8093571	0.90[EUR][1000 genomes]
rs8094172	0.81[ASN][1000 genomes]
rs9710023	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9945339	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9951147	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9959191	0.84[AFR][1000 genomes]
rs9959759	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9961705	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9961851	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9964759	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9967123	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9945374	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs9945374	SPIRE1	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12597800-12634600	Weak transcription	Aorta	Aorta
2	chr18:12602200-12638400	Weak transcription	Fetal Brain Female	brain
3	chr18:12607000-12640200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr18:12607800-12651800	Weak transcription	Brain Germinal Matrix	brain
5	chr18:12608800-12628800	Weak transcription	NH-A	brain
6	chr18:12609200-12629400	Weak transcription	HSMMtube	muscle
7	chr18:12609400-12621400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr18:12609400-12621600	Weak transcription	NHEK	skin
9	chr18:12609400-12628800	Weak transcription	HUVEC	blood vessel
10	chr18:12609600-12629000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:12609800-12622800	Weak transcription	Fetal Brain Male	brain
12	chr18:12611400-12629000	Weak transcription	HSMM	muscle
13	chr18:12611600-12621400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr18:12611600-12621400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:12611600-12629200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:12611800-12630400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr18:12616000-12627400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:12616400-12630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr18:12616400-12640400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr18:12616400-12644800	Weak transcription	Brain Hippocampus Middle	brain
21	chr18:12616600-12621000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:12616600-12645200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr18:12616800-12621200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr18:12616800-12621400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr18:12616800-12625000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr18:12616800-12625000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr18:12616800-12629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr18:12617000-12628800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr18:12617400-12630600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr18:12619600-12629400	Weak transcription	Brain Anterior Caudate	brain

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