Variant report

Variant	rs10820956
Chromosome Location	chr9:94975271-94975272
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	chr9:94907454..94909829-chr9:94972993..94975829,2	MCF-7	breast:
2	chr9:94972713..94975511-chr9:94995305..94997135,2	K562	blood:

Variant related genes	Relation type
ENSG00000238996	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10081693	1.00[ASN][1000 genomes]
rs10119535	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119626	0.81[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];0.85[EUR][1000 genomes]
rs10820954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820962	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820963	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[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	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs10992312	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs10992314	1.00[ASN][1000 genomes]
rs10992334	1.00[ASN][1000 genomes]
rs10992348	1.00[ASN][1000 genomes]
rs12345822	1.00[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12352447	1.00[ASN][1000 genomes]
rs1447114	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.94[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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479413	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036078	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7860297	1.00[ASN][1000 genomes]
rs7863859	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7872739	1.00[ASN][1000 genomes]
rs7873882	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9695754	1.00[CEU][hapmap];1.00[JPT][hapmap];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
rs10820956	CENPP	cis	Esophagus Muscularis	GTEx
rs10820956	CENPP	cis	Artery Tibial	GTEx
rs10820956	NOL8	Cis_1M	lymphoblastoid	RTeQTL
rs10820956	CENPP	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94968800-94976800	Strong transcription	A549	lung
2	chr9:94969000-94975400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:94969600-94976200	Strong transcription	NH-A	brain
4	chr9:94969600-94977000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:94969800-94975400	Strong transcription	Osteobl	bone
6	chr9:94969800-94976400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:94969800-94976800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:94970000-94976600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:94970400-94976000	Strong transcription	Hela-S3	cervix
10	chr9:94970400-94976400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr9:94970400-94976600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:94970400-94976600	Strong transcription	Liver	Liver
13	chr9:94970400-94976600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:94970400-94976800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr9:94970400-94976800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:94970400-94977200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:94970400-94977800	Strong transcription	Primary T cells from cord blood	blood
18	chr9:94970600-94976400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:94970600-94976400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:94970600-94976400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:94970600-94976400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:94970600-94976600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:94970600-94976600	Strong transcription	HMEC	breast
24	chr9:94970800-94975400	Strong transcription	Adipose Nuclei	Adipose
25	chr9:94970800-94975400	Strong transcription	NHLF	lung
26	chr9:94970800-94976000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:94970800-94976000	Strong transcription	HSMMtube	muscle
28	chr9:94970800-94976200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:94970800-94976400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr9:94970800-94976400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:94970800-94976400	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr9:94970800-94976400	Strong transcription	Brain Substantia Nigra	brain
33	chr9:94970800-94976600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:94970800-94976600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr9:94970800-94976600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:94970800-94976600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:94970800-94976600	Strong transcription	Brain Germinal Matrix	brain
38	chr9:94970800-94976600	Strong transcription	Brain Hippocampus Middle	brain
39	chr9:94970800-94976600	Strong transcription	Fetal Thymus	thymus
40	chr9:94970800-94976600	Strong transcription	Dnd41	blood
41	chr9:94970800-94976800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:94970800-94976800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:94970800-94976800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:94970800-94976800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:94970800-94976800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:94970800-94976800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr9:94970800-94976800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr9:94970800-94976800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:94970800-94976800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:94970800-94983400	Weak transcription	Stomach Mucosa	stomach

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