Variant report

Variant	rs10820963
Chromosome Location	chr9:95027436-95027437
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	MYC	chr9:95027429-95027832	MCF10A-Er-Src	breast:	n/a	chr9:95027637-95027646 chr9:95027636-95027645
2	POLR2A	chr9:95023614-95034906	K562	blood:	n/a	n/a
3	MAFK	chr9:95027381-95027705	HepG2	liver:	n/a	chr9:95027525-95027536 chr9:95027523-95027537 chr9:95027638-95027647 chr9:95027520-95027535
4	MAFK	chr9:95027385-95027669	HepG2	liver:	n/a	chr9:95027525-95027536 chr9:95027523-95027537 chr9:95027638-95027647 chr9:95027520-95027535
5	POLR2A	chr9:95027387-95027953	U87	brain:	n/a	n/a
6	POLR2A	chr9:95027435-95027953	U87	brain:	n/a	n/a
7	USF2	chr9:95027372-95027679	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr9:95027291-95027707	HepG2	liver:	n/a	n/a
9	POLR2A	chr9:95026810-95030044	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95025809..95028763-chr9:95033711..95035364,2	MCF-7	breast:
2	chr9:95005657..95008042-chr9:95025879..95028616,2	K562	blood:
3	chr9:95026365..95029765-chr9:95055659..95058477,3	MCF-7	breast:
4	chr9:95026992..95028632-chr9:95044045..95045593,2	MCF-7	breast:
5	chr9:95015646..95017517-chr9:95025518..95027795,2	K562	blood:
6	chr9:95023776..95027446-chr9:95029561..95032473,5	K562	blood:
7	chr9:95019610..95022532-chr9:95024323..95027495,3	K562	blood:
8	chr9:95024617..95027442-chr9:95030716..95033050,2	MCF-7	breast:

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

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

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]
rs10119535	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]
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	1.00[ASN][1000 genomes]
rs10761150	0.82[GIH][hapmap]
rs10820949	0.94[AMR][1000 genomes]
rs10820954	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820961	0.82[GIH][hapmap]
rs10820962	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820970	0.87[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];0.93[LWK][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];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[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];0.88[MKK][hapmap];1.00[YRI][hapmap];0.87[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[ASN][1000 genomes]
rs10992350	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[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	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60993552	1.00[ASN][1000 genomes]
rs6479412	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479413	0.92[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	0.87[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];0.93[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs7873882	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10820963	CENPP	cis	Nerve Tibial	GTEx
rs10820963	CENPP	cis	Esophagus Muscularis	GTEx
rs10820963	NOL8	Cis_1M	lymphoblastoid	RTeQTL
rs10820963	CENPP	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94982800-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:94982800-95045600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:94990200-95054000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:94990400-95038200	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr9:94991200-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:94991200-95052400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:94991200-95053600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:94991400-95050400	Strong transcription	Dnd41	blood
9	chr9:94991400-95052400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:94991400-95053600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:94991400-95053800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:94991400-95053800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:94991800-95053800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:94991800-95054000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:94994000-95053000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:94994200-95038000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:94994400-95038600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:94994600-95051200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr9:94995600-95038000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:94995600-95038600	Strong transcription	Primary T cells from cord blood	blood
21	chr9:94996000-95048600	Strong transcription	Fetal Stomach	stomach
22	chr9:94996200-95051400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr9:94996200-95051400	Strong transcription	Fetal Thymus	thymus
24	chr9:94996200-95052000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:94996400-95051400	Strong transcription	Fetal Muscle Leg	muscle
26	chr9:94996400-95052000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr9:94996600-95035000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:94996600-95038400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr9:94996800-95037400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr9:94996800-95038200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr9:94996800-95042600	Strong transcription	Fetal Brain Female	brain
32	chr9:94997000-95042800	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:94998600-95042800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:94998600-95050600	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr9:94998600-95051200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr9:94998600-95051600	Strong transcription	Adipose Nuclei	Adipose
37	chr9:94998800-95045000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:94998800-95048000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr9:94998800-95049600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:94998800-95050200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:94998800-95051400	Strong transcription	Fetal Intestine Large	intestine
42	chr9:94999000-95038400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr9:94999000-95038600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr9:94999000-95043200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr9:94999000-95048800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:94999400-95051000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr9:94999600-95049600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr9:94999800-95027800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr9:94999800-95048400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr9:95000000-95037800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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