Variant report

Variant	rs72688452
Chromosome Location	chr1:46092365-46092366
allele	A/G
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	POLR2A	chr1:46092282-46092490	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:46092221-46092530	K562	blood:	n/a	n/a
3	POLR2A	chr1:46092203-46092536	K562	blood:	n/a	n/a
4	POLR2A	chr1:46091641-46092847	HepG2	liver:	n/a	n/a
5	CTCF	chr1:46092360-46092510	GM12865	blood:	n/a	n/a
6	POLR2A	chr1:46092295-46092452	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46048860..46051215-chr1:46089890..46092822,3	K562	blood:

Variant related genes	Relation type
CCDC17	TF binding region
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1053941	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579176	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11585275	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587918	0.92[EUR][1000 genomes]
rs11587982	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590549	0.92[EUR][1000 genomes]
rs28412451	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28433203	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28484896	0.92[EUR][1000 genomes]
rs28584711	0.87[EUR][1000 genomes]
rs3014232	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310432	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532639	1.00[ASN][1000 genomes]
rs534534	1.00[ASN][1000 genomes]
rs55659201	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55951835	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020747	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067046	1.00[ASN][1000 genomes]
rs56093189	0.88[EUR][1000 genomes]
rs56238114	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56251392	0.87[EUR][1000 genomes]
rs56261438	1.00[ASN][1000 genomes]
rs58692133	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429573	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662572	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6662999	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671239	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72688460	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517111	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541935	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7553374	1.00[ASN][1000 genomes]
rs9429173	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
3	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs72688452	CCDC163P	cis	Esophagus Mucosa	GTEx
rs72688452	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs72688452	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs72688452	CCDC163P	cis	Stomach	GTEx
rs72688452	CCDC163P	cis	Artery Tibial	GTEx
rs72688452	CCDC163P	cis	lung	GTEx
rs72688452	CCDC163P	cis	Esophagus Muscularis	GTEx
rs72688452	CCDC163P	cis	Whole Blood	GTEx
rs72688452	CCDC163P	cis	Thyroid	GTEx
rs72688452	CCDC163P	cis	Muscle Skeletal	GTEx
rs72688452	CCDC163P	cis	Heart Left Ventricle	GTEx
rs72688452	CCDC163P	cis	Nerve Tibial	GTEx
rs72688452	CCDC163P	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:46070000-46108200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:46071200-46093000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:46071600-46105800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:46074800-46108200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:46076200-46094000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:46077800-46112600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:46078200-46101200	Strong transcription	Thymus	Thymus
10	chr1:46078400-46100800	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:46078800-46101000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:46079000-46100600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:46079600-46094600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:46079800-46109800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:46083200-46093000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:46083200-46094000	Weak transcription	Small Intestine	intestine
17	chr1:46083400-46095000	Weak transcription	Stomach Mucosa	stomach
18	chr1:46083600-46093800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:46083800-46092400	Weak transcription	NHDF-Ad	bronchial
20	chr1:46083800-46093600	Weak transcription	Aorta	Aorta
21	chr1:46084000-46093600	Weak transcription	Fetal Brain Male	brain
22	chr1:46084200-46093200	Weak transcription	Hela-S3	cervix
23	chr1:46084200-46093600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:46084200-46093600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:46084400-46093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:46084400-46094800	Weak transcription	Fetal Kidney	kidney
27	chr1:46084600-46092800	Weak transcription	NH-A	brain
28	chr1:46085200-46093600	Weak transcription	Psoas Muscle	Psoas
29	chr1:46085800-46093400	Weak transcription	HepG2	liver
30	chr1:46086000-46096000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:46087600-46129200	Strong transcription	Fetal Thymus	thymus
32	chr1:46088000-46094400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:46088200-46095200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:46088200-46110000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:46088400-46093400	Weak transcription	HUVEC	blood vessel
36	chr1:46088600-46127400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:46088800-46113400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:46089000-46098600	Weak transcription	Fetal Heart	heart
39	chr1:46089000-46100600	Strong transcription	Fetal Stomach	stomach
40	chr1:46089000-46108800	Strong transcription	Osteobl	bone
41	chr1:46089000-46109400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:46089000-46109400	Strong transcription	Liver	Liver
43	chr1:46089000-46109600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:46089200-46108800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:46089200-46109800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:46089200-46110000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:46089400-46095200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:46089600-46092400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:46089600-46093400	Weak transcription	NHLF	lung
50	chr1:46089600-46093600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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