Variant report

Variant	rs12908300
Chromosome Location	chr15:72357781-72357782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72342663..72345423-chr15:72357313..72359041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223253	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10518979	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1074330	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072338	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072339	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11072346	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11852789	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11853101	0.81[EUR][1000 genomes]
rs11853268	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11858015	0.81[EUR][1000 genomes]
rs12050895	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12439900	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12591426	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12592044	0.90[EUR][1000 genomes]
rs12592364	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12593134	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12593908	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12595228	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12595464	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898585	0.83[AMR][1000 genomes]
rs12899485	0.87[EUR][1000 genomes]
rs12901580	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901886	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902006	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903484	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12903980	0.88[EUR][1000 genomes]
rs12906711	0.94[EUR][1000 genomes]
rs12908882	0.85[EUR][1000 genomes]
rs12911154	0.94[EUR][1000 genomes]
rs12913042	0.86[EUR][1000 genomes]
rs12914070	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12916694	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12916951	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12917428	0.93[EUR][1000 genomes]
rs1384007	0.94[EUR][1000 genomes]
rs16953769	0.85[EUR][1000 genomes]
rs16956302	0.81[EUR][1000 genomes]
rs16956328	0.87[EUR][1000 genomes]
rs16956381	0.88[EUR][1000 genomes]
rs16956444	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16956452	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16956634	0.81[EUR][1000 genomes]
rs2035379	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2054601	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2200056	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279283	0.91[EUR][1000 genomes]
rs2306488	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306490	0.94[EUR][1000 genomes]
rs2415130	0.86[EUR][1000 genomes]
rs2625530	0.81[EUR][1000 genomes]
rs2742323	0.80[EUR][1000 genomes]
rs2856929	0.80[AMR][1000 genomes]
rs2899773	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957368	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2957373	0.80[EUR][1000 genomes]
rs34137768	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34189331	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34487006	0.82[EUR][1000 genomes]
rs34514871	0.84[EUR][1000 genomes]
rs35021156	0.85[EUR][1000 genomes]
rs35112434	0.85[EUR][1000 genomes]
rs35115747	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35167572	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35186252	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35206011	0.81[EUR][1000 genomes]
rs35258998	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35673773	0.92[EUR][1000 genomes]
rs35713471	0.82[EUR][1000 genomes]
rs3743224	0.84[EUR][1000 genomes]
rs3803471	0.80[AMR][1000 genomes]
rs4131630	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4238447	0.81[EUR][1000 genomes]
rs4238449	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4411469	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4445848	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4776579	0.81[EUR][1000 genomes]
rs4776581	0.94[EUR][1000 genomes]
rs4776584	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4776586	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4777464	0.81[EUR][1000 genomes]
rs4777469	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4777471	0.93[EUR][1000 genomes]
rs4777477	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777478	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777480	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4777484	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4777485	0.82[EUR][1000 genomes]
rs4777489	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55854204	0.90[EUR][1000 genomes]
rs62023342	0.88[EUR][1000 genomes]
rs62025574	0.93[EUR][1000 genomes]
rs6494990	0.80[EUR][1000 genomes]
rs71395051	0.92[EUR][1000 genomes]
rs7170461	0.93[EUR][1000 genomes]
rs7170754	0.93[EUR][1000 genomes]
rs7172309	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7183749	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8025504	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8028532	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032038	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8182011	0.82[EUR][1000 genomes]
rs8192386	0.81[EUR][1000 genomes]
rs8192431	0.82[EUR][1000 genomes]
rs972028	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs972029	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	esv11550	chr15:72353301-72395288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12908300	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72301000-72361200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:72339000-72363400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:72350800-72360000	Weak transcription	A549	lung
4	chr15:72351200-72361000	Weak transcription	Fetal Intestine Large	intestine
5	chr15:72351200-72363400	Weak transcription	NHDF-Ad	bronchial
6	chr15:72351200-72395800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:72353200-72361200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:72353600-72379600	Weak transcription	Primary T cells from cord blood	blood
9	chr15:72353800-72366400	Weak transcription	Fetal Kidney	kidney
10	chr15:72354000-72366800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:72354000-72378400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:72354200-72358400	Weak transcription	Fetal Stomach	stomach
13	chr15:72354200-72363000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:72354400-72361200	Weak transcription	Ovary	ovary
15	chr15:72354400-72374800	Weak transcription	Psoas Muscle	Psoas
16	chr15:72355200-72362000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:72355800-72376200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:72356000-72364000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:72356400-72370200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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