Variant report

Variant	rs3810919
Chromosome Location	chr9:116037894-116037895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:507)
CpG islands
(count:61)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:507 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

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	MXI1	chr9:116037083-116038132	H1-hESC	embryonic stem cell:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
3	POLR2A	chr9:116037409-116038302	GM15510	blood:	n/a	n/a
4	REST	chr9:116037011-116038362	H1-neurons	neurons:	n/a	n/a
5	MYC	chr9:116037672-116038248	MCF-7	breast:	n/a	chr9:116037899-116037908
6	POLR2A	chr9:116036438-116039178	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr9:116037426-116038757	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr9:116037351-116038891	HepG2	liver:	n/a	n/a
9	ETS1	chr9:116037474-116038180	K562	blood:	n/a	chr9:116037878-116037889
10	MYC	chr9:116037716-116038111	HUVEC	blood vessel:	n/a	chr9:116037899-116037908
11	ELF1	chr9:116037336-116038089	A549	lung:	n/a	chr9:116037397-116037409
12	TAF1	chr9:116037806-116038123	GM12892	blood:	n/a	n/a
13	POLR2A	chr9:116037243-116038348	K562	blood:	n/a	n/a
14	SIN3AK20	chr9:116037357-116038099	HepG2	liver:	n/a	n/a
15	ZBTB33	chr9:116037256-116038190	SK-N-SH	brain:	n/a	n/a
16	IRF1	chr9:116036651-116038361	K562	blood:	n/a	n/a
17	EGR1	chr9:116037356-116038155	K562	blood:	n/a	chr9:116037569-116037578 chr9:116037847-116037871 chr9:116037568-116037581 chr9:116037568-116037581
18	POLR2A	chr9:116037334-116038302	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr9:116037398-116038356	ProgFib	skin:	n/a	n/a
20	PML	chr9:116037683-116038212	GM12878	blood:	n/a	n/a
21	EP300	chr9:116037818-116038352	K562	blood:	n/a	chr9:116038069-116038085 chr9:116037975-116037988
22	TAF1	chr9:116037322-116038482	A549	lung:	n/a	n/a
23	ZBTB33	chr9:116037513-116038176	HCT-116	colon:	n/a	n/a
24	REST	chr9:116037553-116038379	HL-60	blood:	n/a	n/a
25	USF2	chr9:116037607-116037990	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZBTB33	chr9:116037553-116037954	HCT-116	colon:	n/a	n/a
27	ETS1	chr9:116037468-116038174	A549	lung:	n/a	chr9:116037878-116037889
28	POLR2A	chr9:116037376-116038246	HepG2	liver:	n/a	n/a
29	SIN3AK20	chr9:116037652-116038332	PANC-1	pancreas:	n/a	n/a
30	SP4	chr9:116037570-116038139	H1-hESC	embryonic stem cell:	n/a	chr9:116037879-116037890
31	REST	chr9:116037406-116038185	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr9:116037439-116038223	SK-N-MC	brain:	n/a	n/a
33	ZNF263	chr9:116036824-116038493	HEK293-T-REx	kidney:	n/a	n/a
34	BACH1	chr9:116037634-116038231	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr9:116037285-116038403	ECC-1	luminal epithelium:	n/a	chr9:116037899-116037908
36	POLR2A	chr9:116036883-116039038	H1-hESC	embryonic stem cell:	n/a	n/a
37	ATF2	chr9:116037510-116038333	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr9:116037391-116038427	MCF-7	breast:	n/a	n/a
39	MXI1	chr9:116037251-116038329	HepG2	liver:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
40	CREB1	chr9:116037384-116038337	HepG2	liver:	n/a	n/a
41	YY1	chr9:116037594-116038127	A549	lung:	n/a	n/a
42	ZC3H11A	chr9:116037437-116038256	K562	blood:	n/a	n/a
43	TCF12	chr9:116037343-116038342	A549	lung:	n/a	n/a
44	YY1	chr9:116037577-116038189	HCT-116	colon:	n/a	n/a
45	USF2	chr9:116037132-116038349	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr9:116037372-116038260	U87	brain:	n/a	n/a
47	GABPA	chr9:116037662-116038139	GM12878	blood:	n/a	n/a
48	SIN3AK20	chr9:116036628-116038581	MCF-7	breast:	n/a	n/a
49	BRCA1	chr9:116037539-116038109	H1-hESC	embryonic stem cell:	n/a	n/a
50	GABPA	chr9:116037369-116038100	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:116037885-116037935	ProgFib	skin:	n/a
2	chr9:116037885-116037935	SK-N-SH	brain:	n/a
3	chr9:116037885-116037935	GM12891	blood:	n/a
4	chr9:116037885-116037935	HepG2	liver:	n/a
5	chr9:116037885-116037935	Hela-S3	cervix:	n/a
6	chr9:116037885-116037935	ovcar-3	ovarian:	n/a
7	chr9:116037885-116037935	GM12892	blood:	n/a
8	chr9:116037885-116037935	SKMC	muscle:	n/a
9	chr9:116037885-116037935	GM19239	blood:	n/a
10	chr9:116037885-116037935	H1-hESC	embryonic stem cell:	embryo
11	chr9:116037885-116037935	Caco-2	colon:	n/a
12	chr9:116037885-116037935	HNPCEpiC	eye:	n/a
13	chr9:116037885-116037935	HRPEpiC	eye:	n/a
14	chr9:116037885-116037935	K562	blood:	n/a
15	chr9:116037885-116037935	AG09309	skin:	n/a
16	chr9:116037885-116037935	GM12878	blood:	n/a
17	chr9:116037885-116037935	GM06990	blood:	n/a
18	chr9:116037885-116037935	HCF	heart:	n/a
19	chr9:116037885-116037935	SK-N-SH_RA	brain:	n/a
20	chr9:116037885-116037935	RPTEC	kidney:	n/a
21	chr9:116037885-116037935	MCF-7	breast:	n/a
22	chr9:116037885-116037935	HRCEpiC	kidney:	n/a
23	chr9:116037885-116037935	PANC-1	pancreas:	n/a
24	chr9:116037885-116037935	MCF10A-Er-Src	breast:	n/a
25	chr9:116037885-116037935	Hepatocyte	liver:	n/a
26	chr9:116037885-116037935	HMEC	breast:	n/a
27	chr9:116037885-116037935	HEK293	kidney:	embryo
28	chr9:116037885-116037935	HCM	heart:	n/a
29	chr9:116037885-116037935	PrEC	prostate:	n/a
30	chr9:116037885-116037935	NB4	blood:	n/a
31	chr9:116037885-116037935	HL-60	blood:	n/a
32	chr9:116037885-116037935	ECC-1	luminal epithelium:	n/a
33	chr9:116037885-116037935	AG04450	lung:	fetal
34	chr9:116037885-116037935	NHDF-neo	bronchial:	n/a
35	chr9:116037885-116037935	HRE	kidney:	n/a
36	chr9:116037885-116037935	AG04449	skin:	fetal
37	chr9:116037885-116037935	NH-A	brain:	n/a
38	chr9:116037885-116037935	NT2-D1	testis:	n/a
39	chr9:116037885-116037935	Jurkat	blood:	n/a
40	chr9:116037885-116037935	HPAEpiC	pulmonary alveolar:	n/a
41	chr9:116037885-116037935	SK-N-MC	brain:	n/a
42	chr9:116037885-116037935	BE2_C	brain:	n/a
43	chr9:116037885-116037935	HAEpiC	amniotic membrane:	n/a
44	chr9:116037885-116037935	T-47D	breast:	n/a
45	chr9:116037885-116037935	HEEpiC	esophagus:	n/a
46	chr9:116037885-116037935	PFSK-1	brain:	n/a
47	chr9:116037885-116037935	NHBE	bronchial:	n/a
48	chr9:116037885-116037935	AG09319	gingival:	n/a
49	chr9:116037885-116037935	A549	lung:	n/a
50	chr9:116037885-116037935	AoSMC	blood vessel:	n/a

(count:28 , 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	chr9:115912624..115913401-chr9:116037240..116038163,3	K562	blood:
22	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
23	chr9:116036349..116038748-chr9:116343941..116345814,2	K562	blood:
24	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:
25	chr9:115983488..115985496-chr9:116035418..116038927,3	MCF-7	breast:
26	chr9:116035314..116038256-chr9:116326581..116329349,2	K562	blood:
27	chr14:74485715..74486262-chr9:116037780..116038421,2	Hela-S3	cervix:
28	chr9:116036149..116038435-chr9:116101107..116104521,3	K562	blood:

No data

Variant related genes	Relation type
PRPF4	TF binding region
CDC26	TF binding region
CDC26	CpG island
PRPF4	CpG island
ENSG00000157653	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000114378	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000136709	Chromatin interaction
ENSG00000119636	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000054282	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000140525	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000197889	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000136867	Chromatin interaction
ENSG00000187097	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10116039	0.86[CEU][hapmap]
rs10120404	0.85[EUR][1000 genomes]
rs10123780	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10125030	0.97[EUR][1000 genomes]
rs10817474	0.86[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10817475	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs10981723	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11789775	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11791027	0.81[EUR][1000 genomes]
rs11794214	0.98[EUR][1000 genomes]
rs11794663	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12337498	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12337709	0.98[EUR][1000 genomes]
rs12350705	0.95[EUR][1000 genomes]
rs17763934	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17764013	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17831500	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3087548	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3088235	0.86[CEU][hapmap]
rs3810917	1.00[CEU][hapmap]
rs3810918	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs41307479	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4979229	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4979232	1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7032466	0.81[LWK][hapmap]
rs7847295	0.86[AFR][1000 genomes]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3810919	CDC26	cis	Thyroid	GTEx
rs3810919	CDC26	cis	Muscle Skeletal	GTEx
rs3810919	CDC26	cis	parietal	SCAN
rs3810919	PRPF4	cis	Thyroid	GTEx
rs3810919	CDC26	cis	cerebellum	SCAN
rs3810919	PRPF4	cis	lung	GTEx
rs3810919	ENSG00000136875	cis	multi-tissue	Pritchard
rs3810919	PRPF4	cis	Stomach	GTEx
rs3810919	PRPF4	cis	multi-tissue	Pritchard
rs3810919	CDC26	cis	Heart Left Ventricle	GTEx
rs3810919	ZNF483	cis	cerebellum	SCAN

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	chr9:116036800-116038000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr9:116036800-116038000	Active TSS	Fetal Brain Male	brain
7	chr9:116036800-116038000	Active TSS	Right Ventricle	heart
8	chr9:116036800-116038200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr9:116036800-116038200	Active TSS	Brain Substantia Nigra	brain
10	chr9:116036800-116038400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr9:116036800-116038400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:116036800-116038400	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr9:116036800-116038400	Active TSS	Brain Angular Gyrus	brain
14	chr9:116036800-116038400	Active TSS	Brain Cingulate Gyrus	brain
15	chr9:116036800-116038400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:116036800-116038400	Active TSS	Colonic Mucosa	Colon
17	chr9:116036800-116038400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr9:116036800-116038400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr9:116036800-116038400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr9:116036800-116038400	Active TSS	Fetal Lung	lung
21	chr9:116036800-116038400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr9:116036800-116038400	Active TSS	Thymus	Thymus
23	chr9:116036800-116038600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr9:116036800-116038600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr9:116036800-116038600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr9:116036800-116038600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:116036800-116038600	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr9:116036800-116038600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:116036800-116038600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:116036800-116038600	Active TSS	Muscle Satellite Cultured Cells	--
31	chr9:116036800-116038600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:116036800-116038600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:116036800-116038600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:116036800-116038600	Active TSS	Aorta	Aorta
35	chr9:116036800-116038600	Active TSS	Fetal Intestine Large	intestine
36	chr9:116036800-116038600	Active TSS	Fetal Intestine Small	intestine
37	chr9:116036800-116038600	Active TSS	Fetal Stomach	stomach
38	chr9:116036800-116038600	Active TSS	Fetal Thymus	thymus
39	chr9:116036800-116038600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr9:116036800-116038600	Active TSS	Psoas Muscle	Psoas
41	chr9:116036800-116038600	Active TSS	GM12878-XiMat	blood
42	chr9:116036800-116038600	Active TSS	NHDF-Ad	bronchial
43	chr9:116036800-116038600	Active TSS	NHEK	skin
44	chr9:116036800-116038800	Active TSS	H1 Cell Line	embryonic stem cell
45	chr9:116036800-116038800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:116036800-116038800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:116036800-116038800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:116036800-116038800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:116036800-116038800	Active TSS	Fetal Muscle Trunk	muscle
50	chr9:116036800-116038800	Active TSS	A549	lung

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