Variant report

Variant	rs10119535
Chromosome Location	chr9:95044229-95044230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95043031..95045621-chr9:95049059..95052537,3	MCF-7	breast:
2	chr9:95026992..95028632-chr9:95044045..95045593,2	MCF-7	breast:
3	chr9:95041855..95050591-chr9:95053528..95058799,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239183	Chromatin interaction
ENSG00000196305	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10081693	1.00[ASN][1000 genomes]
rs10117603	0.90[ASN][1000 genomes]
rs10119626	0.87[EUR][1000 genomes]
rs10120980	0.82[GIH][hapmap]
rs10123080	0.91[ASN][1000 genomes]
rs10123342	0.82[GIH][hapmap]
rs10156530	0.91[ASN][1000 genomes]
rs10283718	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10761150	0.82[GIH][hapmap]
rs10820949	0.90[AMR][1000 genomes]
rs10820954	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820956	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]
rs10820961	0.82[GIH][hapmap]
rs10820962	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820963	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820970	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10820973	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10820978	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];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]
rs10992303	0.82[GIH][hapmap]
rs10992308	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]
rs10992312	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]
rs10992314	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10992334	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10992348	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs10992350	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs12345822	1.00[ASN][1000 genomes]
rs12347857	0.90[ASN][1000 genomes]
rs12349712	1.00[ASN][1000 genomes]
rs12352447	1.00[ASN][1000 genomes]
rs1447114	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];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951849	1.00[ASN][1000 genomes]
rs3758229	0.82[GIH][hapmap]
rs3889951	1.00[ASN][1000 genomes]
rs58391046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479413	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036078	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7860297	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7863859	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7872739	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs7873882	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875681	0.90[ASN][1000 genomes]
rs9299403	0.82[GIH][hapmap]
rs9695754	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv972780	chr9:95008644-95049016	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10119535	CENPP	cis	Nerve Tibial	GTEx
rs10119535	IPPK	cis	cerebellum	SCAN
rs10119535	OMD	cis	cerebellum	SCAN
rs10119535	ZNF484	cis	parietal	SCAN
rs10119535	IARS	cis	parietal	SCAN
rs10119535	CENPP	cis	Artery Tibial	GTEx
rs10119535	CENPP	cis	cerebellum	SCAN
rs10119535	CENPP	cis	parietal	SCAN
rs10119535	CENPP	cis	Esophagus Muscularis	GTEx
rs10119535	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	chr9:94982800-95045600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:94990200-95054000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:94991200-95052400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:94991200-95053600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:94991400-95050400	Strong transcription	Dnd41	blood
6	chr9:94991400-95052400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:94991400-95053600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:94991400-95053800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:94991400-95053800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:94991800-95053800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:94991800-95054000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:94994000-95053000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:94994600-95051200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr9:94996000-95048600	Strong transcription	Fetal Stomach	stomach
15	chr9:94996200-95051400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr9:94996200-95051400	Strong transcription	Fetal Thymus	thymus
17	chr9:94996200-95052000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr9:94996400-95051400	Strong transcription	Fetal Muscle Leg	muscle
19	chr9:94996400-95052000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr9:94998600-95050600	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr9:94998600-95051200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr9:94998600-95051600	Strong transcription	Adipose Nuclei	Adipose
23	chr9:94998800-95045000	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:94998800-95048000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:94998800-95049600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:94998800-95050200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:94998800-95051400	Strong transcription	Fetal Intestine Large	intestine
28	chr9:94999000-95048800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:94999400-95051000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr9:94999600-95049600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr9:94999800-95048400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr9:95000400-95048600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:95000400-95048800	Strong transcription	Left Ventricle	heart
34	chr9:95000400-95050800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:95000600-95045000	Strong transcription	Primary B cells from cord blood	blood
36	chr9:95000600-95049000	Strong transcription	Placenta	Placenta
37	chr9:95002600-95054000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:95004600-95046600	Strong transcription	Brain Anterior Caudate	brain
39	chr9:95009000-95053800	Strong transcription	HSMM	muscle
40	chr9:95009600-95054000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:95011400-95044600	Strong transcription	A549	lung
42	chr9:95011600-95052000	Strong transcription	K562	blood
43	chr9:95011800-95051400	Strong transcription	HepG2	liver
44	chr9:95012000-95052200	Strong transcription	GM12878-XiMat	blood
45	chr9:95012200-95047200	Strong transcription	Lung	lung
46	chr9:95015400-95053000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:95015800-95053200	Strong transcription	Hela-S3	cervix
48	chr9:95016800-95046400	Strong transcription	Colon Smooth Muscle	Colon
49	chr9:95019200-95053600	Strong transcription	HUVEC	blood vessel
50	chr9:95028200-95051600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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