Variant report

Variant	rs12898585
Chromosome Location	chr15:72473928-72473929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72466458..72468561-chr15:72471988..72474307,2	MCF-7	breast:
2	chr15:72473291..72475888-chr15:72577722..72579583,2	K562	blood:
3	chr15:72472929..72475065-chr15:72488904..72491028,2	K562	blood:

Variant related genes	Relation type
ENSG00000175318	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1037680	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072338	0.84[AMR][1000 genomes]
rs11072346	0.81[ASN][1000 genomes]
rs11072351	0.81[ASN][1000 genomes]
rs11853101	0.89[EUR][1000 genomes]
rs11853268	0.81[AMR][1000 genomes]
rs11858015	0.88[EUR][1000 genomes]
rs12050895	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12439900	0.84[AMR][1000 genomes]
rs12442886	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591313	0.86[EUR][1000 genomes]
rs12591338	0.86[EUR][1000 genomes]
rs12591426	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12592044	0.83[EUR][1000 genomes]
rs12593908	0.81[ASN][1000 genomes]
rs12901886	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902661	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12903484	0.84[AMR][1000 genomes]
rs12904652	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12908300	0.83[AMR][1000 genomes]
rs12908882	0.83[ASN][1000 genomes]
rs12916951	0.84[AMR][1000 genomes]
rs16953769	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16956444	0.81[AMR][1000 genomes]
rs16956634	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2415130	0.83[EUR][1000 genomes]
rs2607090	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2856929	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2912231	0.80[EUR][1000 genomes]
rs34189331	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34487006	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35112434	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35186252	0.81[EUR][1000 genomes]
rs35206011	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35713471	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743224	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803471	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4238449	0.82[ASN][1000 genomes]
rs4411469	0.82[ASN][1000 genomes]
rs4776586	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4777480	0.84[AMR][1000 genomes]
rs4777489	0.82[ASN][1000 genomes]
rs55854204	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60921026	0.84[ASN][1000 genomes]
rs713048	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7169264	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7182776	0.82[ASN][1000 genomes]
rs7183196	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72733369	0.86[EUR][1000 genomes]
rs8023703	0.83[ASN][1000 genomes]
rs8025504	0.84[AMR][1000 genomes]
rs8192364	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8192386	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8192431	0.88[EUR][1000 genomes];0.83[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	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12898585	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72465000-72476200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr15:72466800-72476200	Weak transcription	Esophagus	oesophagus
3	chr15:72468000-72476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:72468400-72476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:72469000-72475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:72471200-72474200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr15:72471200-72474400	Enhancers	Brain Anterior Caudate	brain
8	chr15:72471800-72476200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:72472000-72474200	Weak transcription	A549	lung
10	chr15:72472000-72476200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:72472200-72475800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:72472200-72476200	Enhancers	Placenta	Placenta
13	chr15:72472400-72475200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:72472400-72476000	Weak transcription	HMEC	breast
15	chr15:72472400-72476200	Weak transcription	Gastric	stomach
16	chr15:72472400-72476200	Weak transcription	Left Ventricle	heart
17	chr15:72472400-72476200	Weak transcription	Pancreas	Pancrea
18	chr15:72472600-72475200	Weak transcription	Spleen	Spleen
19	chr15:72472600-72476200	Weak transcription	Right Ventricle	heart
20	chr15:72472800-72476200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:72473000-72476200	Weak transcription	Lung	lung
22	chr15:72473200-72476000	Enhancers	Hela-S3	cervix
23	chr15:72473200-72476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:72473200-72476200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:72473400-72476000	Enhancers	HepG2	liver
26	chr15:72473400-72476200	Weak transcription	Brain Angular Gyrus	brain
27	chr15:72473400-72476200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:72473600-72475200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:72473600-72476000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:72473600-72476000	Weak transcription	Brain Substantia Nigra	brain
31	chr15:72473600-72476200	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:72473800-72474000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:72473800-72476200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:72473800-72476400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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