Variant report

Variant	rs10992312
Chromosome Location	chr9:95105638-95105639
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	FOS	chr9:95105423-95105724	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr9:95105391-95105679	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr9:95105384-95105721	MCF10A-Er-Src	breast:	n/a	n/a
4	RAD21	chr9:95103676-95105921	SK-N-SH	brain:	n/a	chr9:95105322-95105329 chr9:95103975-95103988
5	FOS	chr9:95105413-95105638	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95104923..95105728-chr9:95201175..95201972,2	MCF-7	breast:
2	chr9:95094639..95096742-chr9:95103960..95106422,2	K562	blood:
3	chr9:95055395..95057599-chr9:95104586..95106334,2	K562	blood:
4	chr9:95104810..95105668-chr9:95396756..95397509,3	MCF-7	breast:
5	chr9:95104863..95105872-chr9:95201522..95202100,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229530	TF binding region
ENSG00000196305	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 17 )

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];0.88[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	0.84[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];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10820970	1.00[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]
rs10992308	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	0.83[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];0.85[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	0.88[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	0.97[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	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
5	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
6	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs10992312	RP11-19J3.3	cis	multi-tissue	Pritchard
rs10992312	CENPP	cis	Adipose Subcutaneous	GTEx
rs10992312	CENPP	cis	Liver	GTEx
rs10992312	CENPP	cis	Esophagus Muscularis	GTEx
rs10992312	ZNF484	cis	parietal	SCAN
rs10992312	CENPP	cis	Artery Tibial	GTEx
rs10992312	CENPP	cis	Muscle Skeletal	GTEx
rs10992312	CENPP	cis	Thyroid	GTEx
rs10992312	CENPP	cis	parietal	SCAN
rs10992312	CENPP	cis	Nerve Tibial	GTEx
rs10992312	OMD	cis	cerebellum	SCAN
rs10992312	AUH	cis	parietal	SCAN
rs10992312	CENPP	cis	cerebellum	SCAN
rs10992312	CENPP	cis	Heart Left Ventricle	GTEx
rs10992312	CENPP	cis	Artery Aorta	GTEx
rs10992312	CENPP	cis	lung	GTEx
rs10992312	IPPK	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95088600-95108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:95088800-95111200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:95088800-95111600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:95089000-95110200	Weak transcription	HSMM	muscle
5	chr9:95089000-95112200	Weak transcription	Adipose Nuclei	Adipose
6	chr9:95089200-95110000	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:95089400-95107000	Weak transcription	Brain Germinal Matrix	brain
8	chr9:95089400-95112000	Weak transcription	NHLF	lung
9	chr9:95089400-95113200	Weak transcription	HUVEC	blood vessel
10	chr9:95089400-95116400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:95089600-95111200	Weak transcription	NHDF-Ad	bronchial
12	chr9:95089600-95121800	Weak transcription	Fetal Heart	heart
13	chr9:95089800-95112000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:95090400-95118200	Weak transcription	HepG2	liver
15	chr9:95091000-95120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:95092200-95109800	Weak transcription	Gastric	stomach
17	chr9:95097400-95112800	Weak transcription	Fetal Intestine Small	intestine
18	chr9:95100200-95112000	Weak transcription	Fetal Lung	lung
19	chr9:95100600-95110400	Weak transcription	Brain Angular Gyrus	brain
20	chr9:95100800-95116600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:95101200-95113000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr9:95101400-95110600	Weak transcription	Hela-S3	cervix
23	chr9:95101600-95106200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:95101600-95116600	Weak transcription	Brain Substantia Nigra	brain
25	chr9:95102000-95110400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:95102000-95113200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:95102000-95114000	Weak transcription	Lung	lung
28	chr9:95102000-95116600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:95102000-95121000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:95102200-95110200	Weak transcription	Spleen	Spleen
31	chr9:95102200-95117600	Weak transcription	Fetal Brain Female	brain
32	chr9:95102200-95121400	Weak transcription	A549	lung
33	chr9:95102400-95105800	Weak transcription	HMEC	breast
34	chr9:95102400-95106000	Weak transcription	Fetal Brain Male	brain
35	chr9:95102400-95111200	Weak transcription	Fetal Stomach	stomach
36	chr9:95102400-95112800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:95102400-95116200	Weak transcription	Aorta	Aorta
38	chr9:95102600-95106800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr9:95102600-95109800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:95102600-95110200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr9:95102600-95110800	Weak transcription	NHEK	skin
42	chr9:95102600-95112600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:95102600-95112600	Weak transcription	Fetal Intestine Large	intestine
44	chr9:95102600-95113000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:95102600-95116200	Weak transcription	Primary T cells from cord blood	blood
46	chr9:95102600-95116400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:95102600-95116400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr9:95102600-95116600	Weak transcription	Thymus	Thymus
49	chr9:95102600-95120800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:95102800-95106000	Weak transcription	Ovary	ovary

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