Variant report

Variant	rs4777589
Chromosome Location	chr15:73402903-73402904
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	chr15:73400733..73403020-chr15:73403252..73405301,2	MCF-7	breast:
2	chr15:73400613..73403499-chr15:73403572..73405490,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10048053	0.81[ASN][1000 genomes]
rs1023924	0.86[CHD][hapmap]
rs1038137	0.83[JPT][hapmap]
rs10438294	0.81[CHD][hapmap];0.84[GIH][hapmap]
rs10467948	0.83[JPT][hapmap]
rs10467949	0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1131854	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs11632639	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11636241	0.89[CHB][hapmap]
rs11639213	0.89[CHB][hapmap]
rs11856922	0.92[CEU][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12050774	0.83[CHD][hapmap]
rs12050848	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12708506	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12899246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12902768	0.83[CHB][hapmap]
rs12907139	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12916928	0.94[ASN][1000 genomes]
rs1479337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1479340	0.83[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs1564345	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs17762516	0.83[ASN][1000 genomes]
rs17762600	0.86[CHD][hapmap]
rs17829830	0.86[CHD][hapmap]
rs17829836	0.84[ASN][1000 genomes]
rs1871385	0.83[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]
rs2010793	0.98[ASN][1000 genomes]
rs2046017	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2127277	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2169951	0.83[JPT][hapmap]
rs2251205	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2415147	0.83[CHB][hapmap]
rs28481558	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28743094	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28842482	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899784	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs35060813	0.95[ASN][1000 genomes]
rs3736510	0.83[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap]
rs3743489	0.88[CHB][hapmap]
rs3784793	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4132535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4132536	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs4777582	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4777583	0.93[ASN][1000 genomes]
rs4777590	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs4777591	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56157337	0.82[ASN][1000 genomes]
rs58060856	0.84[ASN][1000 genomes]
rs62017779	0.81[ASN][1000 genomes]
rs6416501	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6416502	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7164894	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7168555	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs7169083	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs7172021	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7172396	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7173142	0.94[ASN][1000 genomes]
rs7175329	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs747872	0.83[CHB][hapmap]
rs747873	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs7495458	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026121	0.83[JPT][hapmap]
rs8026579	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027588	0.89[CHB][hapmap];0.94[CHD][hapmap]
rs8029106	0.81[ASN][1000 genomes]
rs8035063	0.82[ASN][1000 genomes]
rs8042700	0.83[CHB][hapmap]
rs922516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672588	0.88[CHB][hapmap]
rs9806496	0.83[ASN][1000 genomes]
rs9920186	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription 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	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4777589	MYO9A	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73384600-73409200	Weak transcription	Fetal Lung	lung
2	chr15:73388800-73431200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:73389000-73404000	Weak transcription	Ovary	ovary
4	chr15:73393200-73422400	Weak transcription	Aorta	Aorta
5	chr15:73394000-73403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:73394200-73414800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:73394400-73415000	Weak transcription	Fetal Stomach	stomach
8	chr15:73396000-73406400	Weak transcription	Gastric	stomach
9	chr15:73396400-73444600	Weak transcription	Psoas Muscle	Psoas
10	chr15:73397200-73409200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:73398400-73415000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:73400400-73434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:73401000-73403800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr15:73401200-73409200	Weak transcription	Brain Anterior Caudate	brain
15	chr15:73401200-73414600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:73401200-73414800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:73401200-73423000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:73401200-73428200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:73401400-73403400	Weak transcription	Small Intestine	intestine
20	chr15:73401400-73405800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:73401400-73406400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:73401400-73408800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:73401400-73408800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:73401400-73409000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:73401400-73410600	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:73401400-73413000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:73401400-73419600	Weak transcription	Brain Angular Gyrus	brain
28	chr15:73401400-73422400	Weak transcription	Pancreas	Pancrea
29	chr15:73401400-73422800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
31	chr15:73401600-73405800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:73401600-73413600	Weak transcription	Brain Substantia Nigra	brain
33	chr15:73402200-73403000	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr15:73402400-73406400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:73402600-73403000	Enhancers	Fetal Kidney	kidney
36	chr15:73402600-73404800	Enhancers	Fetal Intestine Large	intestine
37	chr15:73402600-73404800	Enhancers	Fetal Intestine Small	intestine
38	chr15:73402800-73403000	Enhancers	Brain Cingulate Gyrus	brain
39	chr15:73402800-73403200	Enhancers	Duodenum Mucosa	Duodenum

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