Variant report

Variant	rs71351495
Chromosome Location	chr18:12621667-12621668
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: 81 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1105748	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954606	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955162	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[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	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12957283	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12959199	0.81[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	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12965549	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12966082	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12966571	1.00[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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971000	1.00[ASN][1000 genomes]
rs17524639	1.00[ASN][1000 genomes]
rs17525318	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525459	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615525	1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17616124	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34215298	1.00[ASN][1000 genomes]
rs34229934	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34371240	0.81[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	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34859829	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34923819	1.00[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	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35160505	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35190325	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35309605	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35532404	1.00[ASN][1000 genomes]
rs35612342	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	1.00[ASN][1000 genomes]
rs35643117	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35686128	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35744165	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	1.00[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	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	1.00[ASN][1000 genomes]
rs71363149	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs71351495	RP11-861E21.2	cis	Thyroid	GTEx
rs71351495	AP001029.1	cis	Artery Tibial	GTEx
rs71351495	RP11-861E21.1	cis	Artery Tibial	GTEx
rs71351495	SPIRE1	cis	Thyroid	GTEx
rs71351495	SLMO1	cis	Artery Tibial	GTEx

Chromatin state (count:36 , 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	chr18:12609400-12628800	Weak transcription	HUVEC	blood vessel
8	chr18:12609600-12629000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr18:12609800-12622800	Weak transcription	Fetal Brain Male	brain
10	chr18:12611400-12629000	Weak transcription	HSMM	muscle
11	chr18:12611600-12629200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:12611800-12630400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr18:12616000-12627400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr18:12616400-12630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr18:12616400-12640400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr18:12616400-12644800	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:12616600-12645200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr18:12616800-12625000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:12616800-12625000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr18:12616800-12629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr18:12617000-12628800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr18:12617400-12630600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr18:12619600-12629400	Weak transcription	Brain Anterior Caudate	brain
24	chr18:12621000-12622200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr18:12621200-12622400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr18:12621200-12645200	Weak transcription	Fetal Muscle Leg	muscle
27	chr18:12621400-12621800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr18:12621400-12622400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:12621400-12622600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr18:12621400-12623000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr18:12621400-12623000	Enhancers	NHDF-Ad	bronchial
32	chr18:12621600-12621800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr18:12621600-12622400	Enhancers	Hela-S3	cervix
34	chr18:12621600-12622400	Enhancers	K562	blood
35	chr18:12621600-12622400	Enhancers	NHEK	skin
36	chr18:12621600-12623000	Enhancers	Osteobl	bone

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