Variant report

Variant	rs12954606
Chromosome Location	chr18:12575861-12575862
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12568355..12572681-chr18:12573228..12577105,4	K562	blood:
2	chr18:12561120..12563206-chr18:12574921..12576824,2	MCF-7	breast:
3	chr18:12568662..12571031-chr18:12574668..12577642,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1105748	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954350	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955162	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955176	1.00[ASN][1000 genomes]
rs12956026	1.00[ASN][1000 genomes]
rs12956686	1.00[ASN][1000 genomes]
rs12957011	1.00[ASN][1000 genomes]
rs12957283	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958301	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958598	1.00[ASN][1000 genomes]
rs12959199	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[ASN][1000 genomes]
rs12963149	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964717	1.00[ASN][1000 genomes]
rs12965549	1.00[ASN][1000 genomes]
rs12966082	1.00[ASN][1000 genomes]
rs12966571	1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971000	1.00[ASN][1000 genomes]
rs17524639	1.00[ASN][1000 genomes]
rs17525318	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525459	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525599	0.90[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	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17616124	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634564	0.80[AFR][1000 genomes]
rs34054541	1.00[ASN][1000 genomes]
rs34084006	1.00[ASN][1000 genomes]
rs34088731	1.00[ASN][1000 genomes]
rs34180475	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34183067	1.00[ASN][1000 genomes]
rs34215298	1.00[ASN][1000 genomes]
rs34229934	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34371240	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34460164	1.00[ASN][1000 genomes]
rs34469203	1.00[ASN][1000 genomes]
rs34503700	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34512782	1.00[ASN][1000 genomes]
rs34737110	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34859829	1.00[ASN][1000 genomes]
rs34923819	1.00[ASN][1000 genomes]
rs34933611	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35082337	1.00[ASN][1000 genomes]
rs35160505	0.90[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[ASN][1000 genomes]
rs35532404	1.00[ASN][1000 genomes]
rs35612342	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616981	1.00[ASN][1000 genomes]
rs35643117	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35686128	1.00[ASN][1000 genomes]
rs35744165	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35815040	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35826479	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864675	1.00[ASN][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	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[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351492	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351494	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351495	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351501	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353221	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353222	1.00[ASN][1000 genomes]
rs71363149	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
rs12954606	RP11-861E21.2	cis	Thyroid	GTEx
rs12954606	SLMO1	cis	Artery Tibial	GTEx
rs12954606	AP001029.1	cis	Artery Tibial	GTEx
rs12954606	SPIRE1	Cis_1M	lymphoblastoid	RTeQTL
rs12954606	SPIRE1	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12557600-12580800	Weak transcription	Pancreas	Pancrea
2	chr18:12570000-12595600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:12570200-12578400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr18:12570200-12581800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr18:12574400-12576000	Enhancers	HepG2	liver

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