Variant report

Variant	rs9813424
Chromosome Location	chr3:48514223-48514224
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	chr3:48514109-48515043	K562	blood:	n/a	n/a
2	E2F6	chr3:48514168-48514985	K562	blood:	n/a	chr3:48514401-48514412 chr3:48514546-48514555 chr3:48514544-48514553 chr3:48514401-48514412
3	POLR2A	chr3:48514041-48514973	Hela-S3	cervix:	n/a	n/a
4	IRF4	chr3:48514163-48514966	GM12878	blood:	n/a	chr3:48514490-48514511 chr3:48514514-48514535
5	IRF1	chr3:48514194-48514912	K562	blood:	n/a	chr3:48514490-48514511 chr3:48514644-48514658 chr3:48514514-48514535 chr3:48514606-48514620
6	TCF3	chr3:48514161-48514536	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:48513742-48515182	GM12892	blood:	n/a	n/a
8	CREB1	chr3:48514052-48514889	K562	blood:	n/a	chr3:48514543-48514556
9	ZNF143	chr3:48514122-48514924	H1-hESC	embryonic stem cell:	n/a	chr3:48514649-48514659
10	YY1	chr3:48514083-48515065	K562	blood:	n/a	chr3:48514596-48514615 chr3:48514652-48514663
11	CTCF	chr3:48514160-48514310	AG09319	gingival:	n/a	n/a
12	CTCF	chr3:48514180-48514330	HMEC	breast:	n/a	n/a
13	POU2F2	chr3:48514027-48514974	GM12878	blood:	n/a	chr3:48514611-48514623 chr3:48514649-48514661
14	POLR2A	chr3:48514193-48515257	HepG2	liver:	n/a	n/a
15	CTCF	chr3:48514034-48515176	A549	lung:	n/a	chr3:48514749-48514770 chr3:48514750-48514759
16	MAX	chr3:48513900-48515275	A549	lung:	n/a	n/a
17	UBTF	chr3:48514175-48514673	K562	blood:	n/a	n/a
18	CREB1	chr3:48514088-48515385	HepG2	liver:	n/a	chr3:48514543-48514556
19	MAZ	chr3:48514159-48515130	HepG2	liver:	n/a	n/a
20	CTCF	chr3:48514200-48514350	AG04449	skin:	n/a	n/a
21	POLR2A	chr3:48513747-48515186	Hela-S3	cervix:	n/a	n/a
22	MAX	chr3:48514135-48515043	H1-hESC	embryonic stem cell:	n/a	n/a
23	NFIC	chr3:48514084-48514951	ECC-1	luminal epithelium:	n/a	chr3:48514623-48514639
24	ELF1	chr3:48514189-48514944	GM12878	blood:	n/a	chr3:48514649-48514661
25	MAX	chr3:48513945-48514993	GM12878	blood:	n/a	n/a
26	TAL1	chr3:48514215-48514716	K562	blood:	n/a	n/a
27	RCOR1	chr3:48514129-48514847	K562	blood:	n/a	n/a
28	HCFC1	chr3:48514207-48514885	K562	blood:	n/a	n/a
29	POLR2A	chr3:48513989-48514855	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:48514059-48515026	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr3:48513789-48515066	GM12878	blood:	n/a	n/a
32	RELA	chr3:48513987-48514969	GM19099	blood:	n/a	n/a
33	MAX	chr3:48514027-48514733	K562	blood:	n/a	n/a
34	POLR2A	chr3:48514032-48514814	K562	blood:	n/a	n/a
35	POU2F2	chr3:48514097-48514936	GM12891	blood:	n/a	chr3:48514611-48514623 chr3:48514649-48514661
36	TBL1XR1	chr3:48514086-48514726	K562	blood:	n/a	n/a
37	MAX	chr3:48513590-48515117	K562	blood:	n/a	n/a
38	POLR2A	chr3:48513949-48515028	PFSK-1	brain:	n/a	n/a
39	CTCF	chr3:48514206-48514928	IMR90	lung:	n/a	chr3:48514749-48514770 chr3:48514750-48514759
40	BCLAF1	chr3:48514129-48514932	GM12878	blood:	n/a	chr3:48514641-48514654 chr3:48514614-48514627 chr3:48514646-48514655
41	REST	chr3:48513768-48515236	H1-neurons	neurons:	n/a	chr3:48514809-48514822 chr3:48514610-48514623 chr3:48514617-48514627
42	POLR2A	chr3:48514187-48514619	A549	lung:	n/a	n/a
43	POLR2A	chr3:48514153-48515184	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:48513808-48514658	GM12891	blood:	n/a	n/a
45	POLR2A	chr3:48513752-48514971	GM12892	blood:	n/a	n/a
46	ELK1	chr3:48514163-48514718	GM12878	blood:	n/a	n/a
47	MYC	chr3:48514102-48515115	K562	blood:	n/a	n/a
48	POLR2A	chr3:48514098-48515082	HCT-116	colon:	n/a	n/a
49	CTCF	chr3:48514200-48514350	NHDF-neo	bronchial:	n/a	n/a
50	YY1	chr3:48514112-48514598	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48512815..48516100-chr3:48594601..48597600,3	K562	blood:
2	chr3:48506857..48510517-chr3:48512823..48515674,4	MCF-7	breast:
3	chr14:50234420..50235360-chr3:48513609..48514501,2	Hela-S3	cervix:
4	chr3:48512987..48515121-chr3:48538907..48542764,4	MCF-7	breast:
5	chr3:48514107..48516088-chr3:48667675..48669788,2	K562	blood:
6	chr3:48513994..48514495-chr5:114505101..114505601,2	NB4	blood:
7	chr3:48505885..48511674-chr3:48512501..48516993,10	K562	blood:
8	chr3:48281039..48283392-chr3:48513120..48515828,2	K562	blood:
9	chr3:48511787..48515469-chr3:48539737..48543035,4	K562	blood:
10	chr3:48514015..48514728-chr6:3068708..3069290,2	Hela-S3	cervix:
11	chr3:48513069..48515559-chr3:48519678..48521467,2	K562	blood:
12	chr3:48488178..48489912-chr3:48513298..48514956,2	MCF-7	breast:
13	chr3:48512656..48514553-chr3:48541410..48544214,2	K562	blood:
14	chr3:48514041..48514610-chr3:50273546..50274395,2	Hela-S3	cervix:
15	chr12:108954730..108955376-chr3:48513846..48514503,2	Hela-S3	cervix:
16	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:

Variant related genes	Relation type
SHISA5	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000272277	Chromatin interaction
ENSG00000152503	Chromatin interaction
ENSG00000075856	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000165516	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13325221	1.00[AMR][1000 genomes]
rs28789805	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9311427	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841713	0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9845083	1.00[AMR][1000 genomes]
rs9867665	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv590243	chr3:48505831-48519821	Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv590244	chr3:48505924-48519821	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv590245	chr3:48506222-48519821	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48513200-48514600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:48513200-48514600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:48513200-48514800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:48513200-48514800	Active TSS	Hela-S3	cervix
5	chr3:48513200-48515000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr3:48513200-48515000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr3:48513200-48515200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr3:48513400-48514400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr3:48513400-48514400	Active TSS	NH-A	brain
10	chr3:48513400-48514600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr3:48513400-48514600	Active TSS	Rectal Smooth Muscle	rectum
12	chr3:48513400-48514600	Active TSS	NHDF-Ad	bronchial
13	chr3:48513400-48514600	Active TSS	NHLF	lung
14	chr3:48513400-48514800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:48513400-48514800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:48513400-48514800	Active TSS	Brain Hippocampus Middle	brain
17	chr3:48513400-48514800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:48513400-48514800	Active TSS	A549	lung
19	chr3:48513400-48514800	Active TSS	K562	blood
20	chr3:48513400-48515000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr3:48513400-48515000	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr3:48513400-48515000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr3:48513400-48515000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:48513400-48515000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:48513400-48515000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:48513400-48515000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:48513400-48515200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:48513400-48515200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr3:48513400-48515200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:48513600-48514400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:48513600-48514400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:48513600-48514600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:48513600-48514600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr3:48513600-48514600	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr3:48513600-48514600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr3:48513600-48514600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:48513600-48514600	Active TSS	Liver	Liver
38	chr3:48513600-48514600	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:48513600-48514600	Active TSS	Right Atrium	heart
40	chr3:48513600-48514600	Active TSS	Thymus	Thymus
41	chr3:48513600-48514600	Active TSS	Dnd41	blood
42	chr3:48513600-48514600	Active TSS	NHEK	skin
43	chr3:48513600-48514800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:48513600-48514800	Active TSS	Brain Angular Gyrus	brain
45	chr3:48513600-48514800	Active TSS	Brain Anterior Caudate	brain
46	chr3:48513600-48514800	Active TSS	Fetal Intestine Large	intestine
47	chr3:48513600-48514800	Active TSS	Fetal Kidney	kidney
48	chr3:48513600-48514800	Flanking Active TSS	Placenta	Placenta
49	chr3:48513600-48514800	Active TSS	HSMM	muscle
50	chr3:48513600-48515000	Flanking Active TSS	Fetal Muscle Trunk	muscle

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