Variant report

Variant	rs2282068
Chromosome Location	chr9:72873252-72873253
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	POLR2A	chr9:72873200-72874273	GM12892	blood:	n/a	n/a
2	POLR2A	chr9:72873239-72874366	HCT-116	colon:	n/a	n/a
3	MXI1	chr9:72873235-72874496	HepG2	liver:	n/a	n/a
4	E2F6	chr9:72873105-72874295	H1-hESC	embryonic stem cell:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72874227-72874237
5	POLR2A	chr9:72873155-72874555	Hela-S3	cervix:	n/a	n/a
6	MAX	chr9:72873058-72874712	HCT-116	colon:	n/a	chr9:72874255-72874264
7	MAX	chr9:72873069-72874808	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
8	MAX	chr9:72873096-72874600	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
9	ARID3A	chr9:72872805-72873313	K562	blood:	n/a	n/a
10	POLR2A	chr9:72872858-72874429	U87	brain:	n/a	n/a
11	TFAP2C	chr9:72873172-72874542	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr9:72872956-72873443	PFSK-1	brain:	n/a	n/a
13	BATF	chr9:72873122-72873481	GM12878	blood:	n/a	n/a
14	EBF1	chr9:72873045-72873298	GM12878	blood:	n/a	n/a
15	MYC	chr9:72873032-72874620	NB4	blood:	n/a	chr9:72874255-72874264
16	POLR2A	chr9:72872979-72874209	HepG2	liver:	n/a	n/a
17	RELA	chr9:72873238-72874490	GM19099	blood:	n/a	n/a
18	MAX	chr9:72873114-72874532	A549	lung:	n/a	chr9:72874255-72874264
19	MAZ	chr9:72873179-72874585	K562	blood:	n/a	chr9:72874255-72874264
20	RCOR1	chr9:72873224-72874095	K562	blood:	n/a	n/a
21	BCLAF1	chr9:72873088-72874424	GM12878	blood:	n/a	chr9:72873786-72873795 chr9:72873899-72873912
22	HEY1	chr9:72873049-72873478	HepG2	liver:	n/a	n/a
23	UBTF	chr9:72873135-72874495	K562	blood:	n/a	n/a
24	POLR2A	chr9:72872909-72874290	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr9:72873118-72874334	HL-60	blood:	n/a	n/a
26	POLR2A	chr9:72872279-72874875	HepG2	liver:	n/a	n/a
27	MAX	chr9:72872944-72874679	HepG2	liver:	n/a	chr9:72874255-72874264
28	TEAD4	chr9:72872989-72873446	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr9:72873203-72875053	GM12878	blood:	n/a	n/a
30	POLR2A	chr9:72872969-72874616	GM18505	blood:	n/a	n/a
31	POLR2A	chr9:72873084-72874514	GM18951	blood:	n/a	n/a
32	TAF1	chr9:72873236-72874420	A549	lung:	n/a	n/a
33	STAT3	chr9:72873160-72873753	GM12878	blood:	n/a	n/a
34	JUND	chr9:72873191-72874150	H1-hESC	embryonic stem cell:	n/a	chr9:72873676-72873685 chr9:72873805-72873814
35	MAX	chr9:72873116-72874303	H1-hESC	embryonic stem cell:	n/a	chr9:72874255-72874264
36	EGR1	chr9:72873058-72874857	HCT-116	colon:	n/a	chr9:72874254-72874265 chr9:72874247-72874260 chr9:72874256-72874265 chr9:72874253-72874266 chr9:72874253-72874267 chr9:72874252-72874267 chr9:72873899-72873913 chr9:72874253-72874266 chr9:72874254-72874265 chr9:72874253-72874266 chr9:72874191-72874201 chr9:72873841-72873850 chr9:72874255-72874265 chr9:72874255-72874265 chr9:72874254-72874268
37	ATF2	chr9:72873102-72873545	GM12878	blood:	n/a	n/a
38	FOXM1	chr9:72873242-72874535	GM12878	blood:	n/a	n/a
39	MAZ	chr9:72873242-72874570	GM12878	blood:	n/a	chr9:72874255-72874264
40	MAX	chr9:72873060-72874477	K562	blood:	n/a	chr9:72874255-72874264
41	POLR2A	chr9:72872864-72874397	U87	brain:	n/a	n/a
42	TEAD4	chr9:72873138-72873393	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr9:72872963-72874051	K562	blood:	n/a	n/a
44	POLR2A	chr9:72873051-72874367	K562	blood:	n/a	n/a
45	HEY1	chr9:72872940-72874249	HepG2	liver:	n/a	chr9:72873796-72873811 chr9:72873898-72873913
46	MAX	chr9:72873046-72874468	H1-hESC	embryonic stem cell:	n/a	chr9:72874255-72874264
47	POLR2A	chr9:72873113-72874300	K562	blood:	n/a	n/a
48	ZNF143	chr9:72873248-72874506	GM12878	blood:	n/a	chr9:72873950-72873968
49	TBP	chr9:72873096-72874362	HepG2	liver:	n/a	n/a
50	POLR2A	chr9:72870291-72877116	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72872890..72875231-chr9:73027091..73030195,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLF9-3	chr9:72872027-72873730	NONHSAT131810

Variant related genes	Relation type
SMC5	TF binding region
ENSG00000119138	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10868802	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10868806	0.80[JPT][hapmap]
rs11142345	0.85[ASN][1000 genomes]
rs11142351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148858	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3858108	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2282068	KLF9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72869600-72873600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:72869800-72873600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:72870400-72873600	Flanking Active TSS	Osteobl	bone
4	chr9:72870400-72874800	Active TSS	Right Atrium	heart
5	chr9:72870600-72875000	Active TSS	Aorta	Aorta
6	chr9:72870800-72875200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr9:72871000-72876200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:72871800-72875200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:72872000-72875000	Active TSS	Pancreas	Pancrea
10	chr9:72872200-72873400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:72872200-72873400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr9:72872200-72873600	Flanking Active TSS	Fetal Muscle Leg	muscle
13	chr9:72872200-72873600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr9:72872200-72873600	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr9:72872200-72873600	Flanking Active TSS	Dnd41	blood
16	chr9:72872200-72873600	Flanking Active TSS	HMEC	breast
17	chr9:72872200-72873600	Flanking Active TSS	NHEK	skin
18	chr9:72872200-72873800	Flanking Active TSS	NH-A	brain
19	chr9:72872200-72874800	Active TSS	Fetal Muscle Trunk	muscle
20	chr9:72872400-72873400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr9:72872400-72873400	Flanking Active TSS	Fetal Stomach	stomach
22	chr9:72872400-72873600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:72872400-72873600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr9:72872400-72873600	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr9:72872400-72873600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr9:72872600-72873400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
27	chr9:72872600-72873400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:72872600-72873400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr9:72872600-72873600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:72872600-72873600	Flanking Active TSS	NHLF	lung
31	chr9:72872600-72875000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:72872600-72875000	Active TSS	HSMMtube	muscle
33	chr9:72872600-72875600	Active TSS	Brain Cingulate Gyrus	brain
34	chr9:72872800-72873400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr9:72872800-72873400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr9:72872800-72873400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:72872800-72873600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr9:72872800-72873600	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr9:72872800-72873600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:72872800-72873600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:72872800-72873600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:72872800-72873600	Flanking Active TSS	GM12878-XiMat	blood
43	chr9:72872800-72873800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr9:72872800-72873800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr9:72872800-72873800	Active TSS	Brain Germinal Matrix	brain
46	chr9:72872800-72873800	Flanking Active TSS	HUVEC	blood vessel
47	chr9:72872800-72874400	Active TSS	Brain Anterior Caudate	brain
48	chr9:72872800-72874400	Active TSS	Stomach Mucosa	stomach
49	chr9:72872800-72875000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:72872800-72875000	Active TSS	Fetal Intestine Large	intestine

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