Variant report

Variant	rs10992308
Chromosome Location	chr9:95096811-95096812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95056514..95058397-chr9:95095322..95098279,2	K562	blood:
2	chr9:95096545..95099095-chr9:95217061..95218841,2	MCF-7	breast:
3	chr9:95087199..95090041-chr9:95094689..95100000,7	MCF-7	breast:
4	chr9:95086268..95088088-chr9:95096654..95099068,2	K562	blood:
5	chr9:95086552..95088088-chr9:95096253..95098154,2	K562	blood:

Variant related genes	Relation type
ENSG00000188312	Chromatin interaction
ENSG00000198000	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10081693	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117603	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119535	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10123080	0.91[ASN][1000 genomes]
rs10156530	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10283718	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820954	1.00[ASN][1000 genomes]
rs10820956	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs10820962	1.00[ASN][1000 genomes]
rs10820963	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10820970	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820973	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820978	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820982	0.84[EUR][1000 genomes]
rs10992265	0.91[ASN][1000 genomes]
rs10992266	1.00[ASN][1000 genomes]
rs10992267	1.00[ASN][1000 genomes]
rs10992270	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992314	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992334	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10992348	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992350	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992359	0.84[EUR][1000 genomes]
rs12345822	1.00[ASN][1000 genomes]
rs12347857	1.00[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12350198	0.84[EUR][1000 genomes]
rs12352447	1.00[ASN][1000 genomes]
rs1447114	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1951849	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889951	1.00[ASN][1000 genomes]
rs4744140	0.81[EUR][1000 genomes]
rs56168105	0.83[EUR][1000 genomes]
rs58391046	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	1.00[ASN][1000 genomes]
rs6479413	1.00[ASN][1000 genomes]
rs7036078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036459	0.81[EUR][1000 genomes]
rs7037068	0.81[EUR][1000 genomes]
rs7860297	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862677	0.84[EUR][1000 genomes]
rs7863859	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7872739	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873882	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs7875681	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9695754	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];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	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
5	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
6	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10992308	AUH	cis	parietal	SCAN
rs10992308	CENPP	cis	parietal	SCAN
rs10992308	CENPP	cis	Adipose Subcutaneous	GTEx
rs10992308	CENPP	cis	lung	GTEx
rs10992308	CENPP	cis	Nerve Tibial	GTEx
rs10992308	CENPP	cis	Muscle Skeletal	GTEx
rs10992308	CENPP	cis	Heart Left Ventricle	GTEx
rs10992308	CENPP	cis	Artery Tibial	GTEx
rs10992308	OMD	cis	cerebellum	SCAN
rs10992308	CENPP	cis	multi-tissue	Pritchard
rs10992308	ZNF484	cis	parietal	SCAN
rs10992308	CENPP	cis	Artery Aorta	GTEx
rs10992308	IPPK	cis	cerebellum	SCAN
rs10992308	CENPP	cis	Esophagus Muscularis	GTEx
rs10992308	CENPP	cis	Thyroid	GTEx
rs10992308	CENPP	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95088600-95100000	Weak transcription	Spleen	Spleen
2	chr9:95088600-95101000	Weak transcription	Aorta	Aorta
3	chr9:95088600-95103600	Weak transcription	Esophagus	oesophagus
4	chr9:95088600-95104000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:95088600-95108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:95088800-95099800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:95088800-95100000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:95088800-95100000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:95088800-95100000	Weak transcription	Lung	lung
10	chr9:95088800-95100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:95088800-95100400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:95088800-95100400	Weak transcription	Ovary	ovary
13	chr9:95088800-95102000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:95088800-95102600	Weak transcription	Small Intestine	intestine
15	chr9:95088800-95103600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:95088800-95103800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:95088800-95103800	Weak transcription	Pancreas	Pancrea
18	chr9:95088800-95104000	Weak transcription	Left Ventricle	heart
19	chr9:95088800-95111200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:95088800-95111600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:95089000-95097000	Weak transcription	Psoas Muscle	Psoas
22	chr9:95089000-95099800	Weak transcription	Primary B cells from cord blood	blood
23	chr9:95089000-95100000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:95089000-95100000	Weak transcription	Brain Angular Gyrus	brain
25	chr9:95089000-95100000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:95089000-95101000	Weak transcription	Brain Substantia Nigra	brain
27	chr9:95089000-95101200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:95089000-95101400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:95089000-95102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr9:95089000-95102600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr9:95089000-95103200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:95089000-95103600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:95089000-95104000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:95089000-95104000	Weak transcription	HSMMtube	muscle
35	chr9:95089000-95105600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:95089000-95110200	Weak transcription	HSMM	muscle
37	chr9:95089000-95112200	Weak transcription	Adipose Nuclei	Adipose
38	chr9:95089200-95097800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr9:95089200-95099800	Weak transcription	Brain Anterior Caudate	brain
40	chr9:95089200-95100000	Weak transcription	Liver	Liver
41	chr9:95089200-95100000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr9:95089200-95100000	Weak transcription	Fetal Brain Female	brain
43	chr9:95089200-95100600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:95089200-95101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:95089200-95103800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr9:95089200-95110000	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:95089400-95098600	Weak transcription	Primary T cells from cord blood	blood
48	chr9:95089400-95098800	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:95089400-95099000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:95089400-95099400	Weak transcription	Fetal Stomach	stomach

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