Variant report

Variant	rs3759902
Chromosome Location	chr15:72525274-72525275
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:72525141-72525592	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:72520090-72525590	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:72524989-72525491	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:72517556-72525314	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:72517464-72525609	U87	brain:	n/a	n/a
6	POLR2A	chr15:72518883-72525569	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:72501810-72525301	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72523731..72525453-chr15:74219224..74220936,2	MCF-7	breast:
2	chr15:72519310..72525410-chr15:72562881..72568730,22	MCF-7	breast:
3	chr15:72518424..72531344-chr15:72562525..72571046,23	K562	blood:
4	chr15:72523582..72526035-chr15:72559818..72561426,2	K562	blood:
5	chr15:72514333..72526693-chr15:72558323..72568559,52	MCF-7	breast:
6	chr15:72520024..72526293-chr15:72562525..72566333,14	K562	blood:
7	chr15:72509056..72514932-chr15:72519551..72525663,8	K562	blood:

No data

Variant related genes	Relation type
PKM	TF binding region
ENSG00000261801	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1000281	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1035744	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851850	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072349	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11072350	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11630170	0.82[EUR][1000 genomes]
rs11630611	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11633327	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634622	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637611	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11639282	0.84[AMR][1000 genomes]
rs12442886	0.85[AMR][1000 genomes]
rs13858	0.84[AMR][1000 genomes]
rs16956623	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2034879	0.80[AMR][1000 genomes]
rs2052713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278987	0.81[AMR][1000 genomes]
rs2415134	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957742	0.80[AMR][1000 genomes]
rs35603965	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759900	0.86[AMR][1000 genomes]
rs4506844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55679065	0.84[AMR][1000 genomes]
rs55763892	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59975112	0.82[AMR][1000 genomes]
rs62022788	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62022789	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494992	0.86[AMR][1000 genomes]
rs6494997	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7162299	0.81[AMR][1000 genomes]
rs7169264	0.80[AMR][1000 genomes]
rs7170456	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7175197	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7175792	0.88[AMR][1000 genomes]
rs7179427	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7179942	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7183810	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8023703	0.84[AMR][1000 genomes]
rs8023788	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8025939	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8027164	0.81[AMR][1000 genomes]
rs8027647	0.88[EUR][1000 genomes]
rs8031386	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8032222	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8037381	0.80[AMR][1000 genomes]
rs8038007	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040828	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8192362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
rs3759902	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72524000-72525400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:72524400-72529200	Weak transcription	Esophagus	oesophagus
3	chr15:72524400-72529600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:72524400-72529800	Weak transcription	Lung	lung
5	chr15:72524400-72532000	Weak transcription	Brain Angular Gyrus	brain
6	chr15:72524400-72533000	Weak transcription	Gastric	stomach
7	chr15:72524400-72533200	Weak transcription	Ovary	ovary
8	chr15:72524400-72533400	Weak transcription	Pancreas	Pancrea
9	chr15:72524600-72525400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr15:72524600-72525400	Enhancers	Primary hematopoietic stem cells	blood
11	chr15:72524600-72525400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr15:72524600-72525400	Enhancers	Fetal Heart	heart
13	chr15:72524600-72525400	Enhancers	Placenta	Placenta
14	chr15:72524600-72525400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr15:72524600-72525400	Flanking Active TSS	Hela-S3	cervix
16	chr15:72524600-72525600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:72524600-72525600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr15:72524600-72525600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:72524600-72525600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:72524600-72525600	Enhancers	Fetal Muscle Trunk	muscle
21	chr15:72524600-72525600	Enhancers	Fetal Muscle Leg	muscle
22	chr15:72524600-72525600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr15:72524600-72529200	Weak transcription	Right Atrium	heart
24	chr15:72524600-72532200	Weak transcription	Liver	Liver
25	chr15:72524600-72532600	Weak transcription	Right Ventricle	heart
26	chr15:72524600-72533000	Weak transcription	Aorta	Aorta
27	chr15:72524800-72525400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:72524800-72525400	Enhancers	Colonic Mucosa	Colon
29	chr15:72524800-72525400	Enhancers	Stomach Mucosa	stomach
30	chr15:72524800-72525600	Enhancers	Primary T cells fromperipheralblood	blood
31	chr15:72524800-72525600	Enhancers	Fetal Lung	lung
32	chr15:72524800-72525600	Enhancers	Left Ventricle	heart
33	chr15:72524800-72525600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr15:72524800-72525800	Enhancers	Duodenum Mucosa	Duodenum
35	chr15:72524800-72526800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr15:72524800-72528800	Weak transcription	Fetal Brain Female	brain
37	chr15:72524800-72529000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:72524800-72529400	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:72524800-72533000	Weak transcription	Thymus	Thymus
40	chr15:72524800-72533400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:72524800-72533400	Weak transcription	Brain Substantia Nigra	brain
42	chr15:72524800-72533600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:72524800-72551400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:72525000-72525400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:72525000-72525400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
46	chr15:72525000-72525400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:72525000-72525400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr15:72525000-72525400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr15:72525000-72525400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr15:72525000-72525400	Enhancers	GM12878-XiMat	blood

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