Variant report

Variant	rs549099
Chromosome Location	chr9:27194698-27194699
allele	C/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	JUND	chr9:27194292-27195073	HCT-116	colon:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
2	JUND	chr9:27194281-27194914	SK-N-SH	brain:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
3	JUND	chr9:27193966-27194933	SK-N-SH	brain:	n/a	chr9:27194083-27194094 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
4	POLR2A	chr9:27194474-27194854	MCF10A-Er-Src	breast:	n/a	n/a
5	SP1	chr9:27194024-27195033	HCT-116	colon:	n/a	chr9:27194914-27194921
6	NFIC	chr9:27194317-27194974	SK-N-SH	brain:	n/a	n/a
7	FOS	chr9:27194341-27194833	MCF10A-Er-Src	breast:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194583-27194594 chr9:27194610-27194620 chr9:27194614-27194626
8	STAT3	chr9:27194450-27195061	MCF10A-Er-Src	breast:	n/a	chr9:27194878-27194890 chr9:27194874-27194886
9	EP300	chr9:27194456-27194706	SK-N-SH_RA	brain:	n/a	n/a
10	EGR1	chr9:27194364-27194990	HCT-116	colon:	n/a	n/a
11	E2F4	chr9:27194396-27195229	MCF10A-Er-Src	breast:	n/a	chr9:27194960-27194967 chr9:27194957-27194972 chr9:27194956-27194968 chr9:27194742-27194754 chr9:27194959-27194968 chr9:27194960-27194967 chr9:27194960-27194967
12	MYC	chr9:27194424-27194761	MCF10A-Er-Src	breast:	n/a	n/a
13	JUND	chr9:27193946-27194855	Hela-S3	cervix:	n/a	chr9:27194083-27194094 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
14	POLR2A	chr9:27194329-27194873	HCT-116	colon:	n/a	n/a
15	FOS	chr9:27193938-27195492	MCF10A-Er-Src	breast:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194583-27194594 chr9:27194610-27194620 chr9:27194614-27194626
16	USF2	chr9:27194502-27194702	Hela-S3	cervix:	n/a	n/a
17	PBX3	chr9:27194343-27194908	SK-N-SH	brain:	n/a	n/a
18	STAT3	chr9:27194525-27194725	MCF10A-Er-Src	breast:	n/a	n/a
19	CEBPB	chr9:27194367-27194834	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr9:27194307-27195077	U87	brain:	n/a	n/a
21	YY1	chr9:27194453-27194718	HCT-116	colon:	n/a	n/a
22	POLR2A	chr9:27194473-27195905	MCF10A-Er-Src	breast:	n/a	n/a
23	PBX3	chr9:27194354-27194777	SK-N-SH	brain:	n/a	n/a
24	BATF	chr9:27194446-27194714	GM12878	blood:	n/a	chr9:27194607-27194618
25	MAX	chr9:27194354-27195173	HCT-116	colon:	n/a	n/a
26	FOS	chr9:27193931-27195625	MCF10A-Er-Src	breast:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194583-27194594 chr9:27194610-27194620 chr9:27194614-27194626
27	POLR2A	chr9:27194313-27195050	U87	brain:	n/a	n/a
28	STAT3	chr9:27194443-27195106	MCF10A-Er-Src	breast:	n/a	chr9:27194878-27194890 chr9:27194874-27194886
29	FOSL1	chr9:27193803-27195107	HCT-116	colon:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
30	POLR2A	chr9:27194475-27194825	U87	brain:	n/a	n/a
31	CEBPB	chr9:27194317-27195157	HCT-116	colon:	n/a	n/a
32	TCF12	chr9:27194358-27194958	SK-N-SH	brain:	n/a	n/a
33	JUND	chr9:27194228-27194953	HCT-116	colon:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
34	CEBPB	chr9:27194269-27195045	HCT-116	colon:	n/a	n/a
35	STAT3	chr9:27194473-27194764	MCF10A-Er-Src	breast:	n/a	n/a
36	EP300	chr9:27194377-27194725	Hela-S3	cervix:	n/a	n/a
37	CBX3	chr9:27193803-27195211	HCT-116	colon:	n/a	n/a
38	FOS	chr9:27194406-27194783	MCF10A-Er-Src	breast:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194583-27194594 chr9:27194610-27194620 chr9:27194614-27194626
39	FOSL1	chr9:27193842-27195029	HCT-116	colon:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
40	CEBPB	chr9:27194340-27195505	IMR90	lung:	n/a	n/a
41	FOS	chr9:27193942-27195045	HUVEC	blood vessel:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194583-27194594 chr9:27194610-27194620 chr9:27194614-27194626
42	MYC	chr9:27194474-27194718	MCF10A-Er-Src	breast:	n/a	n/a
43	GATA3	chr9:27194259-27194865	SK-N-SH	brain:	n/a	n/a
44	SETDB1	chr9:27194265-27195012	U2OS	brain:	n/a	n/a
45	YY1	chr9:27194454-27194762	SK-N-SH	brain:	n/a	n/a
46	JUN	chr9:27193934-27194811	HUVEC	blood vessel:	n/a	chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194610-27194620 chr9:27194614-27194626
47	MAZ	chr9:27194157-27194822	Hela-S3	cervix:	n/a	n/a
48	KAP1	chr9:27194517-27194820	HEK293	kidney:	n/a	chr9:27194583-27194592
49	SP1	chr9:27194180-27195092	HCT-116	colon:	n/a	chr9:27194914-27194921
50	POLR2A	chr9:27194464-27194782	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RNA5SP280	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1334810	0.86[JPT][hapmap]
rs1360772	0.86[JPT][hapmap]
rs1360773	0.86[JPT][hapmap]
rs1923332	0.91[JPT][hapmap]
rs2145926	0.86[JPT][hapmap]
rs4242670	0.91[JPT][hapmap]
rs491892	0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs510101	0.95[JPT][hapmap]
rs538294	0.91[JPT][hapmap]
rs558897	0.86[JPT][hapmap]
rs560551	0.86[JPT][hapmap]
rs573722	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606342	0.95[JPT][hapmap]
rs638203	0.86[JPT][hapmap]
rs639225	0.86[JPT][hapmap]
rs654494	0.86[JPT][hapmap]
rs655392	0.86[JPT][hapmap]
rs655880	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs671353	0.86[JPT][hapmap]
rs686256	0.95[JPT][hapmap]
rs692946	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv6512	chr9:27155677-27200455	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv892864	chr9:27176554-27296705	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv466335	chr9:27179244-27234029	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv613946	chr9:27179244-27234029	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1009235	chr9:27189804-27196618	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27151000-27229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:27165400-27198200	Weak transcription	Ovary	ovary
3	chr9:27165400-27219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:27166200-27205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:27166200-27229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:27178400-27197200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:27180800-27230600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:27184000-27197800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:27184200-27212600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:27192000-27196800	Enhancers	HUVEC	blood vessel
11	chr9:27192800-27194800	Weak transcription	Right Atrium	heart
12	chr9:27193000-27195000	Weak transcription	Placenta	Placenta
13	chr9:27193000-27203000	Weak transcription	Aorta	Aorta
14	chr9:27193000-27204800	Weak transcription	Lung	lung
15	chr9:27193000-27209000	Weak transcription	Fetal Stomach	stomach
16	chr9:27193000-27212600	Weak transcription	Spleen	Spleen
17	chr9:27193000-27220000	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:27193400-27194800	Weak transcription	Left Ventricle	heart
19	chr9:27193400-27195400	Enhancers	Colon Smooth Muscle	Colon
20	chr9:27193400-27202600	Weak transcription	Adipose Nuclei	Adipose
21	chr9:27193600-27195400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:27193800-27195400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:27193800-27195400	Enhancers	HMEC	breast
24	chr9:27193800-27195600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:27193800-27195800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:27193800-27197200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:27193800-27197200	Enhancers	NHEK	skin
28	chr9:27193800-27197400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:27194000-27195000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr9:27194000-27195200	Enhancers	Rectal Smooth Muscle	rectum
31	chr9:27194000-27195400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:27194000-27195400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:27194000-27195400	Enhancers	HSMM	muscle
34	chr9:27194200-27194800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:27194200-27195200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:27194200-27195400	Enhancers	Hela-S3	cervix
37	chr9:27194200-27195400	Enhancers	NH-A	brain
38	chr9:27194200-27195600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:27194200-27196000	Enhancers	HSMMtube	muscle
40	chr9:27194600-27194800	Enhancers	Psoas Muscle	Psoas
41	chr9:27194600-27195000	Enhancers	NHLF	lung
42	chr9:27194600-27195000	Flanking Active TSS	Osteobl	bone

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