Variant report

Variant	rs10116039
Chromosome Location	chr9:116038180-116038181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:358)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:358 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr9:116036836-116038458	NB4	blood:	n/a	chr9:116037899-116037908
2	POLR2A	chr9:116037409-116038302	GM15510	blood:	n/a	n/a
3	REST	chr9:116037011-116038362	H1-neurons	neurons:	n/a	n/a
4	MYC	chr9:116037672-116038248	MCF-7	breast:	n/a	chr9:116037899-116037908
5	POLR2A	chr9:116036438-116039178	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr9:116037426-116038757	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr9:116037351-116038891	HepG2	liver:	n/a	n/a
8	ETS1	chr9:116037474-116038180	K562	blood:	n/a	chr9:116037878-116037889
9	POLR2A	chr9:116037243-116038348	K562	blood:	n/a	n/a
10	ZBTB33	chr9:116037256-116038190	SK-N-SH	brain:	n/a	n/a
11	IRF1	chr9:116036651-116038361	K562	blood:	n/a	n/a
12	POLR2A	chr9:116037334-116038302	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr9:116037398-116038356	ProgFib	skin:	n/a	n/a
14	PML	chr9:116037683-116038212	GM12878	blood:	n/a	n/a
15	EP300	chr9:116037818-116038352	K562	blood:	n/a	chr9:116038069-116038085 chr9:116037975-116037988
16	TAF1	chr9:116037322-116038482	A549	lung:	n/a	n/a
17	REST	chr9:116037553-116038379	HL-60	blood:	n/a	n/a
18	POLR2A	chr9:116037376-116038246	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr9:116037652-116038332	PANC-1	pancreas:	n/a	n/a
20	REST	chr9:116037406-116038185	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr9:116037439-116038223	SK-N-MC	brain:	n/a	n/a
22	ZNF263	chr9:116036824-116038493	HEK293-T-REx	kidney:	n/a	n/a
23	BACH1	chr9:116037634-116038231	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr9:116037285-116038403	ECC-1	luminal epithelium:	n/a	chr9:116037899-116037908
25	POLR2A	chr9:116036883-116039038	H1-hESC	embryonic stem cell:	n/a	n/a
26	ATF2	chr9:116037510-116038333	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr9:116037391-116038427	MCF-7	breast:	n/a	n/a
28	MXI1	chr9:116037251-116038329	HepG2	liver:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
29	CREB1	chr9:116037384-116038337	HepG2	liver:	n/a	n/a
30	ZC3H11A	chr9:116037437-116038256	K562	blood:	n/a	n/a
31	TCF12	chr9:116037343-116038342	A549	lung:	n/a	n/a
32	YY1	chr9:116037577-116038189	HCT-116	colon:	n/a	n/a
33	USF2	chr9:116037132-116038349	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr9:116037372-116038260	U87	brain:	n/a	n/a
35	SIN3AK20	chr9:116036628-116038581	MCF-7	breast:	n/a	n/a
36	SPI1	chr9:116038162-116038458	K562	blood:	n/a	chr9:116038312-116038325
37	POLR2A	chr9:116037344-116038313	PFSK-1	brain:	n/a	n/a
38	GABPA	chr9:116037498-116038331	HL-60	blood:	n/a	n/a
39	CEBPD	chr9:116037714-116038249	K562	blood:	n/a	n/a
40	RELA	chr9:116037479-116038514	GM10847	blood:	n/a	n/a
41	FOXM1	chr9:116037497-116038307	GM12878	blood:	n/a	n/a
42	CREB1	chr9:116037263-116038217	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr9:116037419-116038240	ECC-1	luminal epithelium:	n/a	n/a
44	ELK4	chr9:116036883-116038241	Hela-S3	cervix:	n/a	n/a
45	MAX	chr9:116037509-116038451	MCF-7	breast:	n/a	chr9:116037899-116037908
46	SPI1	chr9:116037513-116038730	GM12878	blood:	n/a	chr9:116038135-116038148 chr9:116038312-116038325
47	POLR2A	chr9:116036665-116039023	MCF10A-Er-Src	breast:	n/a	n/a
48	MAX	chr9:116037552-116038244	GM12878	blood:	n/a	chr9:116037899-116037908
49	GABPA	chr9:116037295-116038283	K562	blood:	n/a	n/a
50	BCL3	chr9:116037511-116038285	A549	lung:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:89786881..89787560-chr9:116037730..116038230,2	Hela-S3	cervix:
2	chr16:30076519..30077351-chr9:116037411..116038210,2	MCF-7	breast:
3	chr3:50340330..50341202-chr9:116037757..116038408,2	Hela-S3	cervix:
4	chr9:116037849..116040056-chr9:116062437..116065582,3	MCF-7	breast:
5	chr1:243419232..243419735-chr9:116037603..116038455,2	Hela-S3	cervix:
6	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
7	chr2:128568534..128569250-chr9:116037475..116038413,2	NB4	blood:
8	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
9	chr9:116036733..116038262-chr9:116353878..116356485,2	MCF-7	breast:
10	chr10:15001441..15002591-chr9:116037349..116038423,3	Hela-S3	cervix:
11	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
12	chr9:116036612..116039217-chr9:116063138..116067985,4	MCF-7	breast:
13	chr9:116036323..116039598-chr9:116161482..116165034,3	MCF-7	breast:
14	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
15	chr1:145382245..145382948-chr9:116037760..116038415,2	Hela-S3	cervix:
16	chr9:116036740..116039923-chr9:116057646..116061284,5	MCF-7	breast:
17	chr9:116037889..116039423-chr9:116171987..116174165,2	MCF-7	breast:
18	chr9:116036224..116039468-chr9:116162090..116165920,4	MCF-7	breast:
19	chr16:18812479..18813318-chr9:116037697..116038544,2	Hela-S3	cervix:
20	chr9:115982263..115984734-chr9:116036359..116038354,4	MCF-7	breast:
21	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
22	chr9:116036349..116038748-chr9:116343941..116345814,2	K562	blood:
23	chr9:116037991..116040071-chr9:116101087..116104221,4	MCF-7	breast:
24	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:
25	chr9:115983488..115985496-chr9:116035418..116038927,3	MCF-7	breast:
26	chr9:116038056..116040048-chr9:116108621..116111534,2	MCF-7	breast:
27	chr9:116035314..116038256-chr9:116326581..116329349,2	K562	blood:
28	chr14:74485715..74486262-chr9:116037780..116038421,2	Hela-S3	cervix:
29	chr9:116036149..116038435-chr9:116101107..116104521,3	K562	blood:

No data

Variant related genes	Relation type
CDC26	TF binding region
PRPF4	TF binding region
ENSG00000136709	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000119636	Chromatin interaction
ENSG00000114378	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000187097	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000197889	Chromatin interaction
ENSG00000054282	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000140525	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000149925	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10123780	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs10124895	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981693	0.84[GIH][hapmap]
rs10981723	0.85[CEU][hapmap]
rs12337498	0.86[CEU][hapmap]
rs17764013	0.86[CEU][hapmap]
rs2296073	0.81[MKK][hapmap]
rs3087548	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs3810917	0.86[CEU][hapmap]
rs3810918	0.86[CEU][hapmap];0.88[MEX][hapmap]
rs3810919	0.86[CEU][hapmap]
rs4978536	0.82[GIH][hapmap]
rs4979224	0.82[GIH][hapmap]
rs6477997	0.82[GIH][hapmap]
rs9299214	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10116039	CDC26	cis	Esophagus Muscularis	GTEx
rs10116039	PRPF4	cis	Thyroid	GTEx
rs10116039	CDC26	cis	parietal	SCAN
rs10116039	PRPF4	cis	Esophagus Muscularis	GTEx
rs10116039	ZNF618	cis	cerebellum	SCAN
rs10116039	CDC26	cis	cerebellum	SCAN
rs10116039	SVEP1	cis	parietal	SCAN
rs10116039	CDC26	cis	Whole Blood	GTEx
rs10116039	CDC26	cis	Heart Left Ventricle	GTEx
rs10116039	CDC26	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116036600-116038200	Active TSS	Stomach Smooth Muscle	stomach
2	chr9:116036600-116038600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:116036600-116038600	Active TSS	K562	blood
4	chr9:116036600-116038800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:116036800-116038200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr9:116036800-116038200	Active TSS	Brain Substantia Nigra	brain
7	chr9:116036800-116038400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr9:116036800-116038400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:116036800-116038400	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr9:116036800-116038400	Active TSS	Brain Angular Gyrus	brain
11	chr9:116036800-116038400	Active TSS	Brain Cingulate Gyrus	brain
12	chr9:116036800-116038400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:116036800-116038400	Active TSS	Colonic Mucosa	Colon
14	chr9:116036800-116038400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr9:116036800-116038400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr9:116036800-116038400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr9:116036800-116038400	Active TSS	Fetal Lung	lung
18	chr9:116036800-116038400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr9:116036800-116038400	Active TSS	Thymus	Thymus
20	chr9:116036800-116038600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr9:116036800-116038600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr9:116036800-116038600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr9:116036800-116038600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:116036800-116038600	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr9:116036800-116038600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:116036800-116038600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:116036800-116038600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr9:116036800-116038600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:116036800-116038600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:116036800-116038600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:116036800-116038600	Active TSS	Aorta	Aorta
32	chr9:116036800-116038600	Active TSS	Fetal Intestine Large	intestine
33	chr9:116036800-116038600	Active TSS	Fetal Intestine Small	intestine
34	chr9:116036800-116038600	Active TSS	Fetal Stomach	stomach
35	chr9:116036800-116038600	Active TSS	Fetal Thymus	thymus
36	chr9:116036800-116038600	Active TSS	Placenta Amnion	Placenta Amnion
37	chr9:116036800-116038600	Active TSS	Psoas Muscle	Psoas
38	chr9:116036800-116038600	Active TSS	GM12878-XiMat	blood
39	chr9:116036800-116038600	Active TSS	NHDF-Ad	bronchial
40	chr9:116036800-116038600	Active TSS	NHEK	skin
41	chr9:116036800-116038800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr9:116036800-116038800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:116036800-116038800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:116036800-116038800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:116036800-116038800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:116036800-116038800	Active TSS	Fetal Muscle Trunk	muscle
47	chr9:116036800-116038800	Active TSS	A549	lung
48	chr9:116036800-116039000	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr9:116036800-116039000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:116036800-116039000	Active TSS	HSMM	muscle

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