Variant report

Variant	rs7179942
Chromosome Location	chr15:72563074-72563075
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:72562435-72566033	A549	lung:	n/a	chr15:72563158-72563179 chr15:72563169-72563178
2	EGR1	chr15:72562995-72563187	K562	blood:	n/a	n/a
3	POLR2A	chr15:72563069-72563076	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

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	chr15:72548498..72554612-chr15:72558312..72566000,13	MCF-7	breast:
4	chr15:72557492..72560161-chr15:72562709..72565959,3	K562	blood:
5	chr15:72555118..72559591-chr15:72562362..72567008,6	MCF-7	breast:
6	chr15:72520024..72526293-chr15:72562525..72566333,14	K562	blood:
7	chr15:72549975..72552045-chr15:72561335..72563310,2	K562	blood:
8	chr15:72518424..72531344-chr15:72562525..72571046,23	K562	blood:
9	chr15:72561194..72564093-chr15:72666798..72669351,2	MCF-7	breast:
10	chr15:72540888..72544821-chr15:72560401..72563677,4	MCF-7	breast:
11	chr15:72495998..72498558-chr15:72562827..72566042,3	MCF-7	breast:
12	chr15:72541554..72543753-chr15:72562332..72564348,2	K562	blood:
13	chr15:72513653..72518363-chr15:72563063..72568184,5	MCF-7	breast:
14	chr15:72550392..72553636-chr15:72562522..72566048,4	MCF-7	breast:
15	chr15:72562851..72564645-chr15:72977653..72979663,2	K562	blood:

No data

Variant related genes	Relation type
PARP6	TF binding region
ENSG00000137817	Chromatin interaction
ENSG00000260339	Chromatin interaction
ENSG00000213614	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000260729	Chromatin interaction
ENSG00000175202	Chromatin interaction
ENSG00000140463	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	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1035744	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10851850	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072349	0.90[EUR][1000 genomes]
rs11072350	0.91[EUR][1000 genomes]
rs11630170	0.88[EUR][1000 genomes]
rs11630611	0.86[EUR][1000 genomes]
rs11633327	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634622	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11637611	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442886	0.81[EUR][1000 genomes]
rs12904652	0.83[EUR][1000 genomes]
rs13858	0.82[EUR][1000 genomes]
rs16956623	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052713	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278987	0.81[EUR][1000 genomes]
rs2415134	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957365	0.81[EUR][1000 genomes]
rs35603965	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759900	0.83[EUR][1000 genomes]
rs3759902	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4506844	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55763892	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62022788	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62022789	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494992	0.83[EUR][1000 genomes]
rs6494997	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7162299	0.82[EUR][1000 genomes]
rs7164780	0.81[EUR][1000 genomes]
rs7169264	0.83[EUR][1000 genomes]
rs7170456	0.87[EUR][1000 genomes]
rs7175197	0.88[EUR][1000 genomes]
rs7179427	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7183055	0.82[EUR][1000 genomes]
rs7183810	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8023788	0.88[EUR][1000 genomes]
rs8025939	0.88[EUR][1000 genomes]
rs8027164	0.81[EUR][1000 genomes]
rs8027647	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8030815	0.81[EUR][1000 genomes]
rs8032222	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037381	0.82[EUR][1000 genomes]
rs8038007	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040828	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8192362	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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
rs7179942	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72530400-72563400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:72531000-72563400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:72536600-72564000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:72537200-72564200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:72537600-72563400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:72540200-72563200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:72540400-72563400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:72551800-72563200	Strong transcription	Fetal Stomach	stomach
9	chr15:72557000-72563200	Strong transcription	NHEK	skin
10	chr15:72559200-72563400	Weak transcription	HUVEC	blood vessel
11	chr15:72559400-72564200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:72559400-72564200	Weak transcription	Esophagus	oesophagus
13	chr15:72559400-72564200	Weak transcription	Pancreas	Pancrea
14	chr15:72559600-72563400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:72560000-72563200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:72560000-72563400	Weak transcription	Fetal Thymus	thymus
17	chr15:72560000-72563400	Weak transcription	NHLF	lung
18	chr15:72560000-72563600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:72560000-72563800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:72560000-72563800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:72560000-72564000	Weak transcription	Stomach Mucosa	stomach
22	chr15:72560000-72564200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:72560000-72564200	Weak transcription	Aorta	Aorta
24	chr15:72560200-72564000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:72560200-72564200	Weak transcription	Gastric	stomach
26	chr15:72560400-72564200	Weak transcription	Colonic Mucosa	Colon
27	chr15:72560600-72563400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:72560600-72563400	Weak transcription	Psoas Muscle	Psoas
29	chr15:72560600-72564200	Weak transcription	Ovary	ovary
30	chr15:72560800-72563400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:72560800-72563400	Weak transcription	Fetal Kidney	kidney
32	chr15:72561000-72563200	Weak transcription	Liver	Liver
33	chr15:72561000-72563400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:72561000-72563400	Weak transcription	Fetal Intestine Large	intestine
35	chr15:72561000-72563600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:72561000-72563600	Weak transcription	Fetal Lung	lung
37	chr15:72561000-72563600	Weak transcription	Spleen	Spleen
38	chr15:72561000-72564000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:72561000-72564200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:72561200-72563400	Weak transcription	Primary B cells from cord blood	blood
41	chr15:72561200-72563600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:72561200-72563800	Weak transcription	NHDF-Ad	bronchial
43	chr15:72561400-72563400	Weak transcription	Brain Substantia Nigra	brain
44	chr15:72561400-72563400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:72561400-72563400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:72561400-72563600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr15:72561400-72563600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:72561400-72563800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:72561400-72563800	Weak transcription	NH-A	brain
50	chr15:72561400-72564200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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