Variant report

Variant	rs1859440
Chromosome Location	chr12:48427329-48427330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48425840..48427385-chr12:48429084..48431301,2	MCF-7	breast:
2	chr12:48426621..48428717-chr12:48430919..48432434,2	K562	blood:
3	chr12:48421744..48425259-chr12:48425932..48429243,5	MCF-7	breast:
4	chr12:48426470..48428398-chr12:48428806..48432334,3	MCF-7	breast:
5	chr12:48424222..48426815-chr12:48427012..48429829,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10492082	0.93[ASN][1000 genomes]
rs10875726	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10875727	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10875733	0.89[ASN][1000 genomes]
rs11168353	0.80[ASN][1000 genomes]
rs11168354	0.80[ASN][1000 genomes]
rs11168358	0.81[ASN][1000 genomes]
rs11168361	0.90[ASN][1000 genomes]
rs11168363	0.91[ASN][1000 genomes]
rs11168364	0.91[ASN][1000 genomes]
rs11168373	0.89[ASN][1000 genomes]
rs11834818	0.80[ASN][1000 genomes]
rs12426981	0.80[ASN][1000 genomes]
rs17122567	0.81[ASN][1000 genomes]
rs1978161	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2056448	0.90[ASN][1000 genomes]
rs2107640	0.86[EUR][1000 genomes]
rs2240306	0.90[ASN][1000 genomes]
rs2408954	0.91[ASN][1000 genomes]
rs3742075	0.80[ASN][1000 genomes]
rs3825403	0.85[ASN][1000 genomes]
rs4258439	0.85[ASN][1000 genomes]
rs4760678	0.86[EUR][1000 genomes]
rs59667534	0.93[ASN][1000 genomes]
rs7138917	0.85[ASN][1000 genomes]
rs7299704	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs733592	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765260	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs886589	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1859440	RP1-228P16.1	cis	Artery Tibial	GTEx
rs1859440	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48420400-48429000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:48422000-48429000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:48423800-48430600	Weak transcription	Fetal Kidney	kidney
5	chr12:48423800-48430600	Weak transcription	Right Atrium	heart
6	chr12:48424000-48429000	Weak transcription	Fetal Lung	lung
7	chr12:48424200-48430000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:48424200-48430200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48424400-48427400	Weak transcription	Right Ventricle	heart
10	chr12:48424400-48430600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:48424600-48429800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:48424800-48437400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:48425000-48431000	Weak transcription	Fetal Heart	heart
14	chr12:48425200-48431000	Weak transcription	Fetal Intestine Large	intestine
15	chr12:48425400-48429000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:48425400-48430800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:48425600-48429000	Weak transcription	HMEC	breast
18	chr12:48425600-48430600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:48426600-48427400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:48426800-48428600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:48427000-48430600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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