Variant report

Variant	rs2039221
Chromosome Location	chr9:115874261-115874262
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	CTCF	chr9:115874220-115874370	AG09319	gingival:	n/a	n/a
2	CTCF	chr9:115873842-115874376	A549	lung:	n/a	n/a
3	CTCF	chr9:115873864-115874340	MCF-7	breast:	n/a	n/a
4	CTCF	chr9:115874220-115874370	AG04450	lung:	n/a	n/a
5	CTCF	chr9:115873846-115875286	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr9:115874180-115874330	SAEC	small airway:	n/a	n/a
7	SMC3	chr9:115873848-115874439	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr9:115873866-115874267	MCF-7	breast:	n/a	n/a
9	RAD21	chr9:115873846-115874442	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr9:115874147-115874263	GM19240	blood:	n/a	n/a
11	CTCF	chr9:115873850-115874312	HCT-116	colon:	n/a	n/a
12	CTCF	chr9:115874140-115874290	HA-sp	spinal cord:	n/a	n/a
13	CTCF	chr9:115874183-115874402	K562	blood:	n/a	n/a
14	CTCF	chr9:115873850-115874481	HCT-116	colon:	n/a	n/a
15	CTCF	chr9:115873765-115874329	K562	blood:	n/a	chr9:115873826-115873839 chr9:115873826-115873839 chr9:115873825-115873841 chr9:115873824-115873842
16	CTCF	chr9:115874169-115874264	GM12878	blood:	n/a	n/a
17	CTCF	chr9:115874220-115874370	HA-sp	spinal cord:	n/a	n/a
18	CTCF	chr9:115874120-115874270	HUVEC	blood vessel:	n/a	n/a
19	GATA3	chr9:115874128-115874446	T-47D	breast:	n/a	chr9:115874234-115874241 chr9:115874234-115874241 chr9:115874234-115874241

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115687009..115687855-chr9:115874049..115874602,2	MCF-7	breast:
2	chr9:115872624..115875532-chr9:115912017..115913734,2	MCF-7	breast:

Variant related genes	Relation type
FAM225B	TF binding region
FAM225A	TF binding region
ENSG00000136867	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10981635	0.81[ASN][1000 genomes]
rs12236936	0.83[ASN][1000 genomes]
rs12237814	0.81[ASN][1000 genomes]
rs1928977	0.83[ASN][1000 genomes]
rs41280207	0.83[ASN][1000 genomes]
rs4322081	0.81[ASN][1000 genomes]
rs62576104	0.80[EUR][1000 genomes]
rs7031790	0.92[CEU][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs7867889	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv831691	chr9:115754699-115929459	Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv825051	chr9:115811606-115882022	ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv825052	chr9:115811634-115882048	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv893734	chr9:115815398-115891009	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv2757353	chr9:115815398-115892245	ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv2753302	chr9:115819870-115888112	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv893735	chr9:115821854-115891009	ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv2421517	chr9:115852715-115874994	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv893736	chr9:115852715-115891009	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv893737	chr9:115852715-115893229	Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv893738	chr9:115852715-115894240	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1046217	chr9:115854339-115881588	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1042807	chr9:115854339-115883741	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1040513	chr9:115854339-115885060	Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv442164	chr9:115854351-115883753	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	esv2761253	chr9:115854351-115885060	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv893739	chr9:115859223-115891009	Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv893740	chr9:115860251-115891009	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv893741	chr9:115862518-115891009	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv893742	chr9:115867276-115910991	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
25	nsv893743	chr9:115867276-115917783	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115874000-115874400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:115874000-115874400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:115874000-115874400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr9:115874000-115874400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:115874000-115874400	Enhancers	Brain Anterior Caudate	brain
6	chr9:115874000-115874400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr9:115874000-115874400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
8	chr9:115874000-115874400	Active TSS	HSMMtube	muscle
9	chr9:115874000-115874400	Active TSS	NH-A	brain
10	chr9:115874000-115874400	Flanking Active TSS	Osteobl	bone
11	chr9:115874000-115874600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
12	chr9:115874000-115874600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:115874000-115874600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr9:115874000-115874600	Enhancers	Spleen	Spleen
15	chr9:115874000-115875000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr9:115874000-115875000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:115874000-115875000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr9:115874000-115875000	Enhancers	NHEK	skin
19	chr9:115874000-115875200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:115874000-115875200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr9:115874000-115875200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr9:115874000-115875200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:115874000-115875200	Enhancers	Brain Hippocampus Middle	brain
24	chr9:115874000-115875200	Enhancers	HMEC	breast
25	chr9:115874000-115875200	Enhancers	HSMM	muscle
26	chr9:115874200-115874400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:115874200-115874400	Bivalent Enhancer	Placenta	Placenta
28	chr9:115874200-115875200	Enhancers	Adipose Nuclei	Adipose

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