Variant report

Variant	rs2274599
Chromosome Location	chr9:117424855-117424856
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	RAD21	chr9:117424223-117424922	HCT-116	colon:	n/a	chr9:117424710-117424723 chr9:117424908-117424920
2	CTCF	chr9:117424840-117424990	HPF	lung:	n/a	chr9:117424905-117424918
3	TCF12	chr9:117424158-117424899	A549	lung:	n/a	n/a
4	RAD21	chr9:117424196-117424982	A549	lung:	n/a	chr9:117424710-117424723 chr9:117424908-117424920
5	CTCF	chr9:117424820-117424970	K562	blood:	n/a	chr9:117424905-117424918
6	CTCF	chr9:117423988-117425020	SK-N-SH	brain:	n/a	chr9:117424905-117424918
7	RAD21	chr9:117424238-117424899	H1-hESC	embryonic stem cell:	n/a	chr9:117424710-117424723
8	RAD21	chr9:117424240-117424951	MCF-7	breast:	n/a	chr9:117424710-117424723 chr9:117424908-117424920
9	RAD21	chr9:117424299-117424859	ECC-1	luminal epithelium:	n/a	chr9:117424710-117424723
10	SMC3	chr9:117424144-117425226	SK-N-SH	brain:	n/a	n/a
11	CTCF	chr9:117424150-117425170	A549	lung:	n/a	chr9:117424905-117424918
12	RAD21	chr9:117424245-117424970	A549	lung:	n/a	chr9:117424710-117424723 chr9:117424908-117424920
13	CTCF	chr9:117424224-117424960	HCT-116	colon:	n/a	chr9:117424905-117424918
14	CTCF	chr9:117424339-117424866	HCT-116	colon:	n/a	n/a
15	RAD21	chr9:117424367-117424868	IMR90	lung:	n/a	chr9:117424710-117424723
16	RAD21	chr9:117424208-117425004	SK-N-SH	brain:	n/a	chr9:117424710-117424723 chr9:117424908-117424920
17	EBF1	chr9:117424416-117424861	GM12878	blood:	n/a	chr9:117424631-117424642
18	CTCF	chr9:117424840-117424990	Hela-S3	cervix:	n/a	chr9:117424905-117424918
19	SMC3	chr9:117424355-117424978	Hela-S3	cervix:	n/a	n/a
20	RAD21	chr9:117424314-117424865	SK-N-SH_RA	brain:	n/a	chr9:117424710-117424723
21	RAD21	chr9:117424249-117424954	HCT-116	colon:	n/a	chr9:117424710-117424723 chr9:117424908-117424920
22	RAD21	chr9:117424298-117424877	Hela-S3	cervix:	n/a	chr9:117424710-117424723

Variant related genes	Relation type
ENSG00000230054	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10982366	0.82[ASN][1000 genomes]
rs12115626	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12553347	0.85[EUR][1000 genomes]
rs12684990	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1536738	1.00[JPT][hapmap]
rs16930564	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16930587	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16930593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16930630	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16930732	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296946	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2900589	0.85[EUR][1000 genomes]
rs41278677	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41278679	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4979425	1.00[CEU][hapmap]
rs7032258	1.00[JPT][hapmap]
rs7039782	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7044633	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7044802	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7045194	0.88[ASN][1000 genomes]
rs73656195	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
2	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong 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 miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS 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	43 gene(s)	inside rSNPs	diseases
19	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
20	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
21	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS 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	30 gene(s)	inside rSNPs	diseases
22	nsv893766	chr9:117385992-117516418	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv615249	chr9:117394595-117424855	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117416000-117426000	Weak transcription	Brain Anterior Caudate	brain
2	chr9:117418400-117426400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:117418800-117426200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:117420400-117425000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:117424600-117425200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr9:117424600-117425200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr9:117424600-117425200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:117424600-117425200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:117424600-117425200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:117424600-117425200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr9:117424600-117425200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:117424600-117425400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr9:117424600-117425400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr9:117424600-117425400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:117424600-117425400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:117424600-117425400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:117424600-117425400	Enhancers	Brain Hippocampus Middle	brain
18	chr9:117424600-117427400	Enhancers	Brain Substantia Nigra	brain
19	chr9:117424800-117425000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:117424800-117425000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:117424800-117425200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr9:117424800-117425400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr9:117424800-117425400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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