Variant report

Variant	rs6479413
Chromosome Location	chr9:94990015-94990016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94983419..94986395-chr9:94989687..94991728,4	K562	blood:
2	chr9:94987548..94989488-chr9:94989589..94991476,2	MCF-7	breast:
3	chr9:94987677..94991575-chr9:94991944..94994722,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10081693	1.00[ASN][1000 genomes]
rs10119535	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119626	0.82[EUR][1000 genomes]
rs10123080	0.91[ASN][1000 genomes]
rs10156530	0.91[ASN][1000 genomes]
rs10283718	1.00[ASN][1000 genomes]
rs10820949	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10820954	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820956	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820962	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820963	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820970	1.00[ASN][1000 genomes]
rs10820973	1.00[ASN][1000 genomes]
rs10820978	1.00[ASN][1000 genomes]
rs10992265	0.91[ASN][1000 genomes]
rs10992266	1.00[ASN][1000 genomes]
rs10992267	1.00[ASN][1000 genomes]
rs10992270	1.00[ASN][1000 genomes]
rs10992308	1.00[ASN][1000 genomes]
rs10992312	1.00[ASN][1000 genomes]
rs10992314	1.00[ASN][1000 genomes]
rs10992334	1.00[ASN][1000 genomes]
rs10992348	1.00[ASN][1000 genomes]
rs10992350	0.90[ASN][1000 genomes]
rs12345822	1.00[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12352447	1.00[ASN][1000 genomes]
rs1447114	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951849	1.00[ASN][1000 genomes]
rs3889951	1.00[ASN][1000 genomes]
rs58391046	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036078	1.00[ASN][1000 genomes]
rs7860297	1.00[ASN][1000 genomes]
rs7863859	1.00[ASN][1000 genomes]
rs7872739	1.00[ASN][1000 genomes]
rs7873882	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9695754	1.00[ASN][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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6479413	CENPP	cis	Artery Tibial	GTEx
rs6479413	CENPP	cis	Esophagus Muscularis	GTEx
rs6479413	CENPP	cis	Nerve Tibial	GTEx
rs6479413	NOL8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94973800-94990400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:94974000-94999000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:94982800-94990800	Strong transcription	Liver	Liver
4	chr9:94982800-94990800	Strong transcription	Ovary	ovary
5	chr9:94982800-94991000	Strong transcription	Spleen	Spleen
6	chr9:94982800-94991200	Strong transcription	Fetal Stomach	stomach
7	chr9:94982800-94991400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:94982800-94991600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr9:94982800-94992400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:94982800-94992400	Strong transcription	Fetal Muscle Leg	muscle
11	chr9:94982800-94993000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr9:94982800-94993800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr9:94982800-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:94982800-95045600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:94983000-94991400	Strong transcription	Thymus	Thymus
16	chr9:94983200-94990600	Strong transcription	Fetal Intestine Small	intestine
17	chr9:94983200-94991000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:94983200-94991000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:94983200-94992600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:94983600-94990400	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:94983800-94990400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:94984000-95012400	Weak transcription	Stomach Mucosa	stomach
23	chr9:94984200-94990400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr9:94984800-94990400	Weak transcription	Fetal Brain Male	brain
25	chr9:94985000-94990400	Weak transcription	Brain Substantia Nigra	brain
26	chr9:94985200-95001000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:94986000-95000600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:94986600-94990200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:94986600-94990400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:94986800-94990400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr9:94987000-94990400	Weak transcription	Psoas Muscle	Psoas
32	chr9:94987400-94990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:94987600-94990200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:94988200-94990400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:94988400-94990400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:94988400-94990800	Weak transcription	Esophagus	oesophagus
37	chr9:94988400-94990800	Weak transcription	Pancreas	Pancrea
38	chr9:94988400-95000800	Weak transcription	Aorta	Aorta
39	chr9:94988600-94990200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:94988600-94990200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr9:94988600-94990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:94988600-94990200	Weak transcription	Adipose Nuclei	Adipose
43	chr9:94988600-94990200	Weak transcription	Lung	lung
44	chr9:94988600-94990400	Weak transcription	Fetal Lung	lung
45	chr9:94988600-94990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:94988600-94990600	Weak transcription	Right Ventricle	heart
47	chr9:94988600-94991200	Weak transcription	HMEC	breast
48	chr9:94988800-94990200	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:94988800-94990400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr9:94988800-94990400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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