Variant report

Variant	rs4078292
Chromosome Location	chr9:95727458-95727459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95726879..95729699-chr9:95735044..95738591,3	K562	blood:
2	chr9:95726594..95728723-chr9:95769310..95772276,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127084	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10123843	0.86[JPT][hapmap]
rs1022833	0.86[JPT][hapmap]
rs10739933	0.86[JPT][hapmap]
rs10739934	0.86[JPT][hapmap]
rs10821030	0.86[JPT][hapmap]
rs10821035	0.86[JPT][hapmap]
rs10992489	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs12003440	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12003885	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12336022	0.86[JPT][hapmap]
rs12337654	0.86[JPT][hapmap]
rs13284600	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13293147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13294147	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[ASN][1000 genomes]
rs17886128	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296060	0.86[JPT][hapmap]
rs34405247	0.95[ASN][1000 genomes]
rs34739544	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34953814	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35449185	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35721889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4074836	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4260949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744150	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4744151	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4744160	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58264693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479434	0.86[JPT][hapmap]
rs7024752	0.86[ASN][1000 genomes]
rs7032277	0.86[JPT][hapmap]
rs7035881	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7039812	0.86[JPT][hapmap]
rs7040645	0.86[JPT][hapmap]
rs7043469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7856681	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7858810	0.88[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs7859461	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7873125	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9942865	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4078292	CENPP	cis	cerebellum	SCAN
rs4078292	ZNF484	cis	cerebellum	SCAN
rs4078292	ZNF484	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95715400-95732200	Weak transcription	Fetal Brain Female	brain
2	chr9:95720000-95731400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr9:95725400-95728600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr9:95725600-95727600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr9:95725600-95729200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr9:95725600-95734000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr9:95725800-95728000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr9:95725800-95728400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr9:95725800-95728800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:95725800-95729000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:95725800-95729200	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr9:95726000-95728200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr9:95726000-95728200	Active TSS	Duodenum Mucosa	Duodenum
14	chr9:95726000-95728400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:95726000-95728400	Flanking Active TSS	HepG2	liver
16	chr9:95726000-95728600	Active TSS	Rectal Smooth Muscle	rectum
17	chr9:95726000-95728800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:95726000-95728800	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr9:95726200-95728000	Active TSS	Colonic Mucosa	Colon
20	chr9:95726200-95728000	Active TSS	Thymus	Thymus
21	chr9:95726200-95728200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:95726200-95728400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr9:95726200-95728600	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr9:95726200-95728800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:95726400-95727600	Active TSS	Fetal Thymus	thymus
26	chr9:95726400-95727800	Active TSS	Adipose Nuclei	Adipose
27	chr9:95726400-95728200	Active TSS	Primary T cells from cord blood	blood
28	chr9:95726400-95728400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:95726400-95729000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:95726400-95729000	Active TSS	Esophagus	oesophagus
31	chr9:95726400-95730200	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr9:95726600-95727600	Active TSS	Brain Cingulate Gyrus	brain
33	chr9:95726600-95727800	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr9:95726600-95727800	Active TSS	Brain Hippocampus Middle	brain
35	chr9:95726600-95728000	Active TSS	Brain Anterior Caudate	brain
36	chr9:95726600-95728000	Active TSS	Right Atrium	heart
37	chr9:95726600-95728200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:95726600-95728200	Active TSS	Brain Substantia Nigra	brain
39	chr9:95726600-95728200	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr9:95726600-95728400	Active TSS	Pancreas	Pancrea
41	chr9:95726600-95728400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
42	chr9:95726600-95728400	Active TSS	Spleen	Spleen
43	chr9:95726600-95728600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:95726600-95728600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr9:95726600-95728600	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr9:95726600-95728800	Active TSS	Gastric	stomach
47	chr9:95726600-95728800	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr9:95726600-95728800	Active TSS	Small Intestine	intestine
49	chr9:95726600-95729000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:95726600-95729000	Active TSS	Liver	Liver

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