Variant report

Variant	rs62022789
Chromosome Location	chr15:72564492-72564493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr15:72564446-72564858	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr15:72564380-72565408	MCF-7	breast:	n/a	n/a
3	POLR2A	chr15:72564400-72565627	K562	blood:	n/a	n/a
4	UBTF	chr15:72564465-72565463	K562	blood:	n/a	n/a
5	MAX	chr15:72564427-72565549	HCT-116	colon:	n/a	chr15:72565030-72565046 chr15:72565026-72565039 chr15:72565028-72565037 chr15:72565028-72565038 chr15:72565027-72565038 chr15:72565029-72565036 chr15:72565027-72565038 chr15:72565028-72565037
6	POLR2A	chr15:72564125-72565544	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:72564142-72565403	Hela-S3	cervix:	n/a	n/a
8	REST	chr15:72564062-72565733	H1-neurons	neurons:	n/a	chr15:72565206-72565219 chr15:72564789-72564802 chr15:72565141-72565154
9	POLR2A	chr15:72564369-72565528	GM19193	blood:	n/a	n/a
10	MAX	chr15:72564451-72565429	NB4	blood:	n/a	chr15:72565030-72565046 chr15:72565026-72565039 chr15:72565028-72565037 chr15:72565028-72565038 chr15:72565027-72565038 chr15:72565029-72565036 chr15:72565027-72565038 chr15:72565028-72565037
11	ELF1	chr15:72564366-72565531	GM12878	blood:	n/a	n/a
12	ZBTB7A	chr15:72564374-72564602	K562	blood:	n/a	n/a
13	POLR2A	chr15:72564440-72565563	GM12891	blood:	n/a	n/a
14	CTCF	chr15:72562435-72566033	A549	lung:	n/a	chr15:72563158-72563179 chr15:72563169-72563178
15	MAX	chr15:72564243-72565497	Hela-S3	cervix:	n/a	chr15:72565030-72565046 chr15:72565026-72565039 chr15:72565028-72565037 chr15:72565028-72565038 chr15:72565027-72565038 chr15:72565029-72565036 chr15:72565027-72565038 chr15:72565028-72565037
16	HCFC1	chr15:72564082-72565924	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr15:72564315-72565398	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr15:72564480-72564630	HMEC	breast:	n/a	n/a
19	POLR2A	chr15:72564450-72565613	U87	brain:	n/a	n/a
20	POLR2A	chr15:72564103-72565550	MCF10A-Er-Src	breast:	n/a	n/a
21	HA-E2F1	chr15:72564209-72565491	MCF-7	breast:	n/a	chr15:72565154-72565163 chr15:72565105-72565114 chr15:72564500-72564510 chr15:72564501-72564509 chr15:72564501-72564509
22	POLR2A	chr15:72564370-72565534	GM18951	blood:	n/a	n/a
23	RUNX3	chr15:72564205-72564647	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:72564437-72565589	GM12892	blood:	n/a	n/a
25	POLR2A	chr15:72564204-72565491	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr15:72564363-72565440	MCF-7	breast:	n/a	n/a
27	SIN3AK20	chr15:72564374-72565470	PANC-1	pancreas:	n/a	n/a
28	BHLHE40	chr15:72564278-72565594	K562	blood:	n/a	chr15:72564787-72564803 chr15:72565064-72565080
29	POLR2A	chr15:72564432-72565484	K562	blood:	n/a	n/a
30	TCF12	chr15:72564000-72565644	A549	lung:	n/a	n/a
31	POLR2A	chr15:72564411-72565741	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr15:72564480-72565483	HUVEC	blood vessel:	n/a	n/a
33	SIN3AK20	chr15:72563917-72565620	MCF-7	breast:	n/a	n/a
34	RCOR1	chr15:72564349-72565643	K562	blood:	n/a	n/a
35	POLR2A	chr15:72564476-72565470	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr15:72564447-72565613	U87	brain:	n/a	n/a
37	POLR2A	chr15:72564216-72565532	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr15:72564418-72565447	A549	lung:	n/a	n/a
39	POLR2A	chr15:72564396-72565590	SK-N-MC	brain:	n/a	n/a
40	MTA3	chr15:72564229-72565621	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:72564232-72565486	H1-neurons	neurons:	n/a	n/a
42	MAX	chr15:72564264-72565453	K562	blood:	n/a	chr15:72565030-72565046 chr15:72565026-72565039 chr15:72565028-72565037 chr15:72565028-72565038 chr15:72565027-72565038 chr15:72565029-72565036 chr15:72565027-72565038 chr15:72565028-72565037
43	SMARCC2	chr15:72564204-72566355	Hela-S3	cervix:	n/a	n/a
44	MAX	chr15:72564170-72565733	A549	lung:	n/a	chr15:72565030-72565046 chr15:72565026-72565039 chr15:72565028-72565037 chr15:72565028-72565038 chr15:72565027-72565038 chr15:72565029-72565036 chr15:72565027-72565038 chr15:72565028-72565037
45	POLR2A	chr15:72564353-72565502	Raji	blood:	n/a	n/a
46	UBTF	chr15:72564341-72565408	K562	blood:	n/a	n/a
47	MAX	chr15:72564468-72565468	ECC-1	luminal epithelium:	n/a	chr15:72565030-72565046 chr15:72565026-72565039 chr15:72565028-72565037 chr15:72565028-72565038 chr15:72565027-72565038 chr15:72565029-72565036 chr15:72565027-72565038 chr15:72565028-72565037
48	MYC	chr15:72564282-72565635	NB4	blood:	n/a	chr15:72565030-72565046 chr15:72565026-72565039 chr15:72565028-72565037 chr15:72565028-72565038 chr15:72565027-72565038 chr15:72565029-72565036 chr15:72565027-72565038 chr15:72565028-72565037
49	SIN3A	chr15:72564321-72565429	GM12878	blood:	n/a	chr15:72564656-72564667
50	POLR2A	chr15:72564417-72565478	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:72514333..72526693-chr15:72558323..72568559,52	MCF-7	breast:
2	chr15:72519310..72525410-chr15:72562881..72568730,22	MCF-7	breast:
3	chr15:72409322..72412006-chr15:72563414..72566011,3	MCF-7	breast:
4	chr15:72548498..72554612-chr15:72558312..72566000,13	MCF-7	breast:
5	chr15:72563307..72566923-chr15:72766066..72767771,3	K562	blood:
6	chr15:72459821..72461687-chr15:72564383..72566445,2	MCF-7	breast:
7	chr15:72557492..72560161-chr15:72562709..72565959,3	K562	blood:
8	chr15:72555118..72559591-chr15:72562362..72567008,6	MCF-7	breast:
9	chr15:72498640..72500862-chr15:72563465..72565516,2	MCF-7	breast:
10	chr15:72520024..72526293-chr15:72562525..72566333,14	K562	blood:
11	chr15:72518424..72531344-chr15:72562525..72571046,23	K562	blood:
12	chr15:72563307..72566923-chr15:72766066..72767771,5	K562	blood:
13	chr15:72563468..72565339-chr15:73075771..73077281,2	MCF-7	breast:
14	chr15:72495998..72498558-chr15:72562827..72566042,3	MCF-7	breast:
15	chr15:72410053..72410729-chr15:72564212..72565118,2	Hela-S3	cervix:
16	chr15:72537383..72539855-chr15:72564362..72566037,2	MCF-7	breast:
17	chr1:28973807..28976760-chr15:72563147..72565838,2	MCF-7	breast:
18	chr15:72513653..72518363-chr15:72563063..72568184,5	MCF-7	breast:
19	chr15:72550392..72553636-chr15:72562522..72566048,4	MCF-7	breast:
20	chr15:72562851..72564645-chr15:72977653..72979663,2	K562	blood:

Variant related genes	Relation type
PARP6	TF binding region
ENSG00000175202	Chromatin interaction
ENSG00000066933	Chromatin interaction
ENSG00000159322	Chromatin interaction
ENSG00000175318	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000166192	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1000281	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1035744	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851850	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072349	0.89[EUR][1000 genomes]
rs11072350	0.91[EUR][1000 genomes]
rs11630170	0.87[EUR][1000 genomes]
rs11630611	0.85[EUR][1000 genomes]
rs11633327	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11634622	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637611	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442886	0.81[EUR][1000 genomes]
rs12904652	0.83[EUR][1000 genomes]
rs13858	0.82[EUR][1000 genomes]
rs16956623	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052713	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278987	0.80[EUR][1000 genomes]
rs2415134	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957365	0.80[EUR][1000 genomes]
rs35603965	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759900	0.82[EUR][1000 genomes]
rs3759902	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4506844	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55763892	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62022788	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494992	0.83[EUR][1000 genomes]
rs6494997	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162299	0.81[EUR][1000 genomes]
rs7164780	0.80[EUR][1000 genomes]
rs7169264	0.83[EUR][1000 genomes]
rs7170456	0.87[EUR][1000 genomes]
rs7175197	0.87[EUR][1000 genomes]
rs7179427	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7179942	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7183055	0.82[EUR][1000 genomes]
rs7183810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023788	0.87[EUR][1000 genomes]
rs8025939	0.87[EUR][1000 genomes]
rs8027164	0.80[EUR][1000 genomes]
rs8027647	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8030815	0.80[EUR][1000 genomes]
rs8032222	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8037381	0.81[EUR][1000 genomes]
rs8038007	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040828	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8192362	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1601	chr15:72549885-72585176	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62022789	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72563600-72564600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr15:72563600-72565600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr15:72563600-72565600	Active TSS	Psoas Muscle	Psoas
4	chr15:72563800-72564600	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr15:72563800-72564600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr15:72563800-72564600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr15:72563800-72564600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:72563800-72564600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:72563800-72564600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr15:72563800-72564600	Flanking Active TSS	HUVEC	blood vessel
11	chr15:72563800-72565400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr15:72563800-72565400	Active TSS	NHDF-Ad	bronchial
13	chr15:72563800-72565600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:72564000-72564600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr15:72564000-72564600	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr15:72564000-72564600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:72564000-72564600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:72564000-72564600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr15:72564000-72564600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:72564000-72564600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr15:72564000-72564600	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr15:72564000-72564600	Active TSS	Right Atrium	heart
23	chr15:72564000-72564800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr15:72564000-72565200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:72564000-72565200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:72564000-72565200	Active TSS	Fetal Muscle Trunk	muscle
27	chr15:72564000-72565400	Active TSS	H1 Cell Line	embryonic stem cell
28	chr15:72564000-72565400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:72564000-72565400	Active TSS	Colon Smooth Muscle	Colon
30	chr15:72564000-72565400	Active TSS	Fetal Intestine Small	intestine
31	chr15:72564000-72565400	Active TSS	GM12878-XiMat	blood
32	chr15:72564000-72565400	Active TSS	HSMM	muscle
33	chr15:72564000-72565400	Active TSS	NHLF	lung
34	chr15:72564000-72565600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr15:72564000-72565600	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr15:72564000-72565600	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr15:72564000-72565800	Active TSS	Brain Germinal Matrix	brain
38	chr15:72564200-72564600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr15:72564200-72564600	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr15:72564200-72564600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr15:72564200-72564600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:72564200-72564600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:72564200-72564600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:72564200-72564600	Flanking Active TSS	Fetal Thymus	thymus
45	chr15:72564200-72564600	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr15:72564200-72564800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:72564200-72565000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:72564200-72565000	Active TSS	Fetal Heart	heart
49	chr15:72564200-72565000	Active TSS	Gastric	stomach
50	chr15:72564200-72565200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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