Variant report

Variant	rs3810918
Chromosome Location	chr9:116036566-116036567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:116036438-116039178	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr9:116036026-116037453	A549	lung:	n/a	n/a
3	CTCF	chr9:116036500-116036650	GM12874	blood:	n/a	n/a
4	POLR2A	chr9:116036286-116038980	GM12891	blood:	n/a	n/a
5	ZNF143	chr9:116036487-116038353	K562	blood:	n/a	chr9:116037848-116037866 chr9:116037852-116037871 chr9:116037344-116037354
6	CHD1	chr9:116035600-116039131	IMR90	lung:	n/a	n/a
7	RAD21	chr9:116036238-116039041	SK-N-SH	brain:	n/a	chr9:116037583-116037595 chr9:116038010-116038023
8	CTCF	chr9:116036520-116036670	HFF-Myc	foreskin:	n/a	n/a
9	MXI1	chr9:116036564-116038986	SK-N-SH	brain:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
10	POLR2A	chr9:116036540-116038499	PBDE	blood:	n/a	n/a
11	JUN	chr9:116036238-116038372	K562	blood:	n/a	n/a
12	CTCF	chr9:116035968-116038774	SK-N-SH	brain:	n/a	n/a
13	CHD1	chr9:116036518-116037487	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr9:116036332-116039038	IMR90	lung:	n/a	n/a
15	RAD21	chr9:116036472-116037289	HCT-116	colon:	n/a	n/a
16	KAP1	chr9:116036378-116038076	U2OS	brain:	n/a	chr9:116036760-116036768
17	HCFC1	chr9:116036232-116038897	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr9:116036521-116037087	IMR90	lung:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116035093..116036761-chr9:116347708..116350133,2	K562	blood:
2	chr9:116035655..116037372-chr9:116289546..116291507,2	K562	blood:
3	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
4	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
5	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
6	chr9:116036423..116037332-chr9:116419975..116420491,2	K562	blood:
7	chr9:116036369..116037533-chr9:116417343..116418092,4	K562	blood:
8	chr9:116036323..116039598-chr9:116161482..116165034,3	MCF-7	breast:
9	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
10	chr9:116036224..116039468-chr9:116162090..116165920,4	MCF-7	breast:
11	chr9:116035030..116037849-chr9:116344314..116346129,2	K562	blood:
12	chr9:115982263..115984734-chr9:116036359..116038354,4	MCF-7	breast:
13	chr9:116036482..116037335-chr9:116168680..116169652,2	MCF-7	breast:
14	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
15	chr9:116036349..116038748-chr9:116343941..116345814,2	K562	blood:
16	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:
17	chr9:115983488..115985496-chr9:116035418..116038927,3	MCF-7	breast:
18	chr9:116035314..116038256-chr9:116326581..116329349,2	K562	blood:
19	chr9:116036149..116038435-chr9:116101107..116104521,3	K562	blood:

No data

Variant related genes	Relation type
PRPF4	TF binding region
ENSG00000119321	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000136868	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10116039	0.86[CEU][hapmap];0.88[MEX][hapmap]
rs10120404	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125030	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125032	0.89[AFR][1000 genomes]
rs10513190	1.00[CHB][hapmap]
rs10817474	0.86[CEU][hapmap]
rs10981723	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs11789775	0.92[EUR][1000 genomes]
rs11793978	1.00[CHB][hapmap]
rs11794214	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11794663	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12337498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12337709	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12342489	0.88[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs12350705	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16931988	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs17763351	1.00[CHB][hapmap]
rs17763934	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17764013	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17831500	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2233913	1.00[CHB][hapmap]
rs3087548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3088235	0.86[CEU][hapmap]
rs3810917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs3810919	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs41307479	0.81[EUR][1000 genomes]
rs4979229	0.98[EUR][1000 genomes];0.95[ASN][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3810918	CDC26	cis	Heart Left Ventricle	GTEx
rs3810918	PRPF4	cis	lung	GTEx
rs3810918	CDC26	cis	parietal	SCAN
rs3810918	CDC26	cis	Thyroid	GTEx
rs3810918	CDC26	cis	Muscle Skeletal	GTEx
rs3810918	PRPF4	cis	Thyroid	GTEx
rs3810918	PRPF4	cis	Stomach	GTEx
rs3810918	ZNF483	cis	cerebellum	SCAN
rs3810918	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs3810918	CDC26	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
3	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:116033800-116036800	Weak transcription	Psoas Muscle	Psoas
6	chr9:116034200-116036600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:116034400-116036600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:116034400-116037000	Weak transcription	Small Intestine	intestine
9	chr9:116034600-116036600	Weak transcription	Brain Germinal Matrix	brain
10	chr9:116034800-116036600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:116035200-116036600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:116035200-116036800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:116035200-116036800	Weak transcription	Aorta	Aorta
14	chr9:116035200-116036800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr9:116035200-116036800	Weak transcription	Right Ventricle	heart
16	chr9:116035200-116036800	Weak transcription	Thymus	Thymus
17	chr9:116035200-116037000	Weak transcription	Lung	lung
18	chr9:116035200-116037000	Weak transcription	Ovary	ovary
19	chr9:116035200-116037200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:116035400-116036600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:116035400-116036600	Weak transcription	Brain Substantia Nigra	brain
22	chr9:116035400-116036600	Weak transcription	Fetal Intestine Small	intestine
23	chr9:116035400-116036800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:116035400-116036800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:116035400-116036800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:116035400-116037000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:116035400-116037000	Weak transcription	Left Ventricle	heart
28	chr9:116035400-116037000	Weak transcription	Pancreas	Pancrea
29	chr9:116035400-116037200	Weak transcription	Spleen	Spleen
30	chr9:116035600-116036600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:116035600-116036600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:116035600-116036600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:116035800-116036600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:116035800-116036600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:116035800-116036600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:116035800-116036600	Enhancers	Fetal Brain Male	brain
37	chr9:116035800-116036600	Weak transcription	HSMMtube	muscle
38	chr9:116035800-116036600	Weak transcription	NH-A	brain
39	chr9:116035800-116036600	Weak transcription	NHDF-Ad	bronchial
40	chr9:116035800-116036800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:116035800-116036800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr9:116035800-116036800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr9:116035800-116036800	Weak transcription	Colonic Mucosa	Colon
44	chr9:116035800-116036800	Weak transcription	Fetal Thymus	thymus
45	chr9:116035800-116037000	Weak transcription	Gastric	stomach
46	chr9:116036000-116036600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:116036000-116036600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:116036000-116036600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:116036000-116036600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr9:116036000-116036600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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