Variant report

Variant	rs11730088
Chromosome Location	chr4:15683968-15683969
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr4:15682843-15684158	K562	blood:	n/a	n/a
2	POLR2A	chr4:15682746-15684156	MCF-7	breast:	n/a	n/a
3	USF2	chr4:15682948-15684071	Hela-S3	cervix:	n/a	n/a
4	IKZF1	chr4:15682973-15684400	GM12878	blood:	n/a	n/a
5	E2F4	chr4:15682349-15684777	MCF10A-Er-Src	breast:	n/a	chr4:15683240-15683251 chr4:15682723-15682732
6	POLR2A	chr4:15682752-15684192	HUVEC	blood vessel:	n/a	n/a
7	BHLHE40	chr4:15683926-15684173	K562	blood:	n/a	n/a
8	POLR2A	chr4:15682612-15684712	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr4:15682658-15684957	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr4:15683864-15684117	GM12878	blood:	n/a	n/a
11	GABPA	chr4:15682904-15684133	MCF-7	breast:	n/a	n/a
12	TAF1	chr4:15682626-15683976	A549	lung:	n/a	n/a
13	POLR2A	chr4:15682803-15684022	HUVEC	blood vessel:	n/a	n/a
14	CHD1	chr4:15682763-15684170	GM12878	blood:	n/a	n/a
15	CHD2	chr4:15682878-15683980	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAFK	chr4:15683797-15684291	K562	blood:	n/a	n/a
17	POLR2A	chr4:15682812-15684032	GM15510	blood:	n/a	n/a
18	KAP1	chr4:15682859-15684035	U2OS	brain:	n/a	n/a
19	MAZ	chr4:15682805-15683968	K562	blood:	n/a	chr4:15682839-15682846
20	POLR2A	chr4:15682734-15684180	ProgFib	skin:	n/a	n/a
21	TBP	chr4:15682829-15684190	K562	blood:	n/a	n/a
22	POLR2A	chr4:15682729-15683973	HCT-116	colon:	n/a	n/a
23	CHD1	chr4:15682231-15684731	H1-hESC	embryonic stem cell:	n/a	n/a
24	MYC	chr4:15683866-15684980	MCF10A-Er-Src	breast:	n/a	n/a
25	RELA	chr4:15682891-15684026	GM18505	blood:	n/a	n/a
26	POLR2A	chr4:15682764-15683968	GM18951	blood:	n/a	n/a
27	POLR2A	chr4:15682735-15684414	HL-60	blood:	n/a	n/a
28	ELF1	chr4:15682767-15684053	HCT-116	colon:	n/a	n/a
29	POLR2A	chr4:15682769-15684036	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr4:15682794-15684245	GM18505	blood:	n/a	n/a
31	IRF1	chr4:15682750-15684537	K562	blood:	n/a	n/a
32	TBP	chr4:15682668-15684400	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr4:15682743-15684299	GM12878	blood:	n/a	n/a
34	TAF1	chr4:15683140-15684056	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr4:15682775-15684526	H1-hESC	embryonic stem cell:	n/a	n/a
36	IRF1	chr4:15682970-15684315	K562	blood:	n/a	n/a
37	MXI1	chr4:15682757-15684082	GM12878	blood:	n/a	n/a
38	RELA	chr4:15682927-15683993	GM19099	blood:	n/a	n/a
39	POLR2A	chr4:15682659-15684186	U87	brain:	n/a	n/a
40	POLR2A	chr4:15682912-15686646	K562	blood:	n/a	n/a
41	POLR2A	chr4:15682794-15684280	GM19099	blood:	n/a	n/a
42	REST	chr4:15683130-15684134	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr4:15682765-15684635	GM12891	blood:	n/a	n/a
44	UBTF	chr4:15682803-15683981	K562	blood:	n/a	n/a
45	RCOR1	chr4:15683038-15684270	GM12878	blood:	n/a	n/a
46	CCNT2	chr4:15682806-15683987	K562	blood:	n/a	n/a
47	CEBPB	chr4:15682860-15684417	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr4:15682734-15684115	GM12878	blood:	n/a	n/a
49	SIN3AK20	chr4:15682660-15684006	MCF-7	breast:	n/a	n/a
50	MTA3	chr4:15682986-15683976	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:15681714..15684664-chr4:16226494..16229781,3	K562	blood:
2	chr4:15003674..15005700-chr4:15682740..15684585,3	K562	blood:
3	chr4:15681678..15685124-chr4:15685309..15687808,5	MCF-7	breast:
4	chr4:15682398..15684850-chr8:101964333..101966529,2	MCF-7	breast:
5	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
6	chr4:15652080..15658606-chr4:15677363..15685579,17	MCF-7	breast:
7	chr4:15655595..15658742-chr4:15680185..15687360,10	MCF-7	breast:
8	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:
9	chr4:15479910..15482087-chr4:15683434..15685124,3	MCF-7	breast:

No data

Variant related genes	Relation type
FAM200B	TF binding region
FBXL5	TF binding region
ENSG00000169762	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000048342	Chromatin interaction
ENSG00000137449	Chromatin interaction
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction
ENSG00000263327	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10005305	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008878	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10015827	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10017222	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10025875	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10433813	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11722300	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722854	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11729955	0.81[CEU][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732953	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11947383	0.80[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13134177	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17405811	0.81[CEU][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28394730	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28604503	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3775956	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4554069	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6449152	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6815296	0.81[CEU][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827406	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6848779	0.81[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434484	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9994518	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3361772	chr4:15666732-15684418	Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11730088	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15679400-15685400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:15679400-15685600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:15679600-15684200	Active TSS	GM12878-XiMat	blood
4	chr4:15679600-15685400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:15679600-15685600	Active TSS	A549	lung
6	chr4:15680200-15685000	Active TSS	K562	blood
7	chr4:15680400-15684200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:15680800-15684800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr4:15681000-15685400	Active TSS	NH-A	brain
10	chr4:15681200-15684200	Active TSS	NHDF-Ad	bronchial
11	chr4:15681400-15684400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:15681400-15684600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:15681400-15684600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:15681400-15684800	Active TSS	Thymus	Thymus
15	chr4:15681600-15684400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr4:15681600-15684600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:15681600-15684600	Active TSS	HSMM	muscle
18	chr4:15681600-15684800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:15681600-15684800	Active TSS	Fetal Thymus	thymus
20	chr4:15681600-15685400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:15681800-15684000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr4:15681800-15684400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr4:15681800-15684600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:15681800-15684600	Active TSS	NHEK	skin
25	chr4:15681800-15685600	Active TSS	NHLF	lung
26	chr4:15681800-15686200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr4:15682000-15684000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:15682000-15684200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:15682000-15684400	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:15682000-15684400	Active TSS	Placenta	Placenta
31	chr4:15682000-15684600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:15682000-15685200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:15682000-15685200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:15682000-15685400	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr4:15682000-15685600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:15682000-15685600	Active TSS	HMEC	breast
37	chr4:15682200-15684200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:15682200-15684200	Active TSS	Fetal Stomach	stomach
39	chr4:15682200-15684400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:15682200-15684400	Active TSS	Muscle Satellite Cultured Cells	--
41	chr4:15682200-15684400	Active TSS	Placenta Amnion	Placenta Amnion
42	chr4:15682200-15684400	Active TSS	Osteobl	bone
43	chr4:15682200-15684600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:15682200-15684800	Active TSS	Fetal Intestine Small	intestine
45	chr4:15682400-15684000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:15682400-15684000	Active TSS	Dnd41	blood
47	chr4:15682400-15684200	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr4:15682400-15684200	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr4:15682400-15684200	Active TSS	HUVEC	blood vessel
50	chr4:15682400-15685000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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