Variant report

Variant	rs9349564
Chromosome Location	chr6:13316024-13316025
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13310952..13313118-chr6:13315206..13317513,2	K562	blood:
2	chr6:13315003..13316712-chr6:13317056..13320082,3	K562	blood:
3	chr6:13314962..13317954-chr6:13328559..13330250,2	K562	blood:
4	chr6:13312615..13316148-chr6:13327198..13329955,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs13203254	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs202016	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202017	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202018	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202019	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202021	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202022	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202023	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20499	0.82[ASN][1000 genomes]
rs20500	0.80[ASN][1000 genomes]
rs2439534	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439535	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439537	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439539	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439540	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439541	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439542	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439543	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439544	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439545	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439548	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439549	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458300	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458309	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458310	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458311	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458312	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458313	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2458314	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2496140	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496142	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496144	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496145	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496147	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496148	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496149	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496151	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496152	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496153	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496154	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496156	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496157	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2919685	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919686	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001966	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001967	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001968	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs364493	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3817737	0.80[ASN][1000 genomes]
rs3817738	0.80[ASN][1000 genomes]
rs3817741	0.80[ASN][1000 genomes]
rs3817742	0.80[ASN][1000 genomes]
rs402705	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs449727	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452309	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488297	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59639740	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs641758	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9381884	0.80[ASN][1000 genomes]
rs9395602	0.80[ASN][1000 genomes]
rs957175	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957176	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9349564	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
3	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:13298200-13326800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:13299600-13326600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:13299800-13326400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:13300200-13327000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:13301200-13325400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:13303800-13327800	Weak transcription	Stomach Mucosa	stomach
13	chr6:13304400-13316800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:13304400-13327800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:13304600-13325600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:13304600-13326200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:13305200-13316400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:13305200-13325800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:13305400-13326200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr6:13305800-13319000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:13305800-13326200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:13307200-13326200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:13307400-13326400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:13308600-13326400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:13308600-13326400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:13309000-13320200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:13309000-13325800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:13309200-13319200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:13309400-13326400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:13309600-13318400	Weak transcription	Fetal Heart	heart
31	chr6:13310200-13325600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr6:13310200-13326400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr6:13310600-13319200	Weak transcription	A549	lung
34	chr6:13311200-13325800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr6:13311200-13325800	Strong transcription	Adipose Nuclei	Adipose
36	chr6:13311200-13326000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:13311200-13326200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:13311400-13325800	Strong transcription	Left Ventricle	heart
39	chr6:13311400-13326000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr6:13311400-13326200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:13311400-13326200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:13311400-13326200	Strong transcription	Fetal Thymus	thymus
43	chr6:13311400-13326400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr6:13311400-13326400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:13311400-13327000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:13311600-13325800	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:13311600-13326000	Strong transcription	Dnd41	blood
48	chr6:13311600-13326200	Strong transcription	Liver	Liver
49	chr6:13312200-13326400	Strong transcription	Primary B cells from cord blood	blood
50	chr6:13312600-13318800	Weak transcription	Muscle Satellite Cultured Cells	--

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