Variant report

Variant	rs10120404
Chromosome Location	chr9:116036125-116036126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:116036026-116037453	A549	lung:	n/a	n/a
2	CTCF	chr9:116036060-116036210	HPAF	blood vessel:	n/a	n/a
3	CHD1	chr9:116035600-116039131	IMR90	lung:	n/a	n/a
4	CTCF	chr9:116035968-116038774	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr9:116036060-116036210	GM12872	blood:	n/a	n/a

No data

(count:10 , 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	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
4	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
5	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
6	chr9:116035030..116037849-chr9:116344314..116346129,2	K562	blood:
7	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
8	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:
9	chr9:115983488..115985496-chr9:116035418..116038927,3	MCF-7	breast:
10	chr9:116035314..116038256-chr9:116326581..116329349,2	K562	blood:

No data

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

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10123780	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125030	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11794214	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11794663	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12337498	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12337709	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12350705	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17763934	0.84[ASN][1000 genomes]
rs3087548	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3810918	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810919	0.85[EUR][1000 genomes]
rs4979229	0.85[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10120404	PRPF4	cis	Stomach	GTEx
rs10120404	CDC26	cis	Thyroid	GTEx
rs10120404	PRPF4	cis	Thyroid	GTEx
rs10120404	CDC26	cis	Heart Left Ventricle	GTEx
rs10120404	PRPF4	cis	lung	GTEx
rs10120404	CDC26	cis	Muscle Skeletal	GTEx
rs10120404	CDC26	cis	Skin Sun Exposed Lower leg	GTEx

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	chr9:116027200-116036200	Strong transcription	Primary T cells from cord blood	blood
6	chr9:116027800-116036200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:116028400-116036200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:116031600-116036200	Strong transcription	Brain Hippocampus Middle	brain
9	chr9:116033600-116036400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:116033800-116036800	Weak transcription	Psoas Muscle	Psoas
11	chr9:116034200-116036200	Weak transcription	HSMM	muscle
12	chr9:116034200-116036400	Weak transcription	Fetal Kidney	kidney
13	chr9:116034200-116036600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:116034400-116036400	Weak transcription	Fetal Heart	heart
15	chr9:116034400-116036600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:116034400-116037000	Weak transcription	Small Intestine	intestine
17	chr9:116034600-116036200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:116034600-116036600	Weak transcription	Brain Germinal Matrix	brain
19	chr9:116034800-116036400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:116034800-116036600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:116035200-116036400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:116035200-116036400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:116035200-116036400	Weak transcription	HUVEC	blood vessel
24	chr9:116035200-116036600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:116035200-116036800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:116035200-116036800	Weak transcription	Aorta	Aorta
27	chr9:116035200-116036800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:116035200-116036800	Weak transcription	Right Ventricle	heart
29	chr9:116035200-116036800	Weak transcription	Thymus	Thymus
30	chr9:116035200-116037000	Weak transcription	Lung	lung
31	chr9:116035200-116037000	Weak transcription	Ovary	ovary
32	chr9:116035200-116037200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:116035400-116036200	Weak transcription	A549	lung
34	chr9:116035400-116036400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:116035400-116036400	Weak transcription	Fetal Brain Female	brain
36	chr9:116035400-116036600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:116035400-116036600	Weak transcription	Brain Substantia Nigra	brain
38	chr9:116035400-116036600	Weak transcription	Fetal Intestine Small	intestine
39	chr9:116035400-116036800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr9:116035400-116036800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:116035400-116036800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:116035400-116037000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:116035400-116037000	Weak transcription	Left Ventricle	heart
44	chr9:116035400-116037000	Weak transcription	Pancreas	Pancrea
45	chr9:116035400-116037200	Weak transcription	Spleen	Spleen
46	chr9:116035600-116036200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr9:116035600-116036200	Weak transcription	GM12878-XiMat	blood
48	chr9:116035600-116036400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:116035600-116036400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:116035600-116036400	Weak transcription	Brain Cingulate Gyrus	brain

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