Variant report

Variant	rs553983496
Chromosome Location	chr9:2230474-2230475
allele	C/T
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	chr9:2230420-2230570	SAEC	small airway:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
2	CTCF	chr9:2230420-2230570	NHEK	skin:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
3	CTCF	chr9:2230400-2230550	HEEpiC	esophagus:	n/a	n/a
4	RAD21	chr9:2230339-2230767	HCT-116	colon:	n/a	chr9:2230538-2230557
5	CTCF	chr9:2230385-2230677	GM12878	blood:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
6	RAD21	chr9:2230442-2230704	Hela-S3	cervix:	n/a	chr9:2230538-2230557
7	RAD21	chr9:2230269-2230876	HCT-116	colon:	n/a	chr9:2230538-2230557
8	RAD21	chr9:2230344-2230714	H1-hESC	embryonic stem cell:	n/a	chr9:2230538-2230557
9	CTCF	chr9:2230440-2230590	BE2_C	brain:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
10	CTCF	chr9:2230374-2230803	HCT-116	colon:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
11	ZNF143	chr9:2230425-2230663	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr9:2230400-2230550	MCF-7	breast:	n/a	n/a
13	CTCF	chr9:2230460-2230610	HMEC	breast:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
14	RAD21	chr9:2230296-2230654	H1-hESC	embryonic stem cell:	n/a	chr9:2230538-2230557
15	CTCF	chr9:2230440-2230590	RPTEC	kidney:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
16	RAD21	chr9:2230400-2230716	H1-hESC	embryonic stem cell:	n/a	chr9:2230538-2230557
17	CTCF	chr9:2230460-2230610	SAEC	small airway:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
18	RAD21	chr9:2230413-2230655	SK-N-SH_RA	brain:	n/a	chr9:2230538-2230557
19	CTCF	chr9:2230380-2230530	HRPEpiC	eye:	n/a	n/a
20	CTCF	chr9:2230459-2230618	LNCaP	prostate:	n/a	chr9:2230540-2230553 chr9:2230537-2230555
21	RAD21	chr9:2230398-2230682	ECC-1	luminal epithelium:	n/a	chr9:2230538-2230557
22	RAD21	chr9:2230385-2230734	A549	lung:	n/a	chr9:2230538-2230557
23	CTCF	chr9:2230460-2230644	LNCaP	prostate:	n/a	chr9:2230540-2230553 chr9:2230537-2230555

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2229879..2232148-chr9:2238435..2240178,2	K562	blood:
2	chr9:2229721..2232093-chr9:2241469..2243158,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL592P	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv892057	chr9:2144687-2241994	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv892059	chr9:2198627-2255397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1033628	chr9:2215179-2303623	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv539927	chr9:2215179-2303623	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892060	chr9:2218129-2261944	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv6457	chr9:2228493-2271756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv892061	chr9:2229694-2262889	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2223600-2240800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:2227400-2234400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:2227800-2231400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:2227800-2231600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:2227800-2231600	Weak transcription	Ovary	ovary
6	chr9:2227800-2234400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:2228000-2231000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr9:2228000-2231200	Weak transcription	Osteobl	bone
9	chr9:2228000-2231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:2228000-2234600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:2228800-2234200	Weak transcription	NHEK	skin
12	chr9:2229000-2230800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:2229200-2230800	Weak transcription	Spleen	Spleen
14	chr9:2229400-2231000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:2229400-2234400	Weak transcription	Placenta	Placenta
16	chr9:2229600-2230800	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:2229800-2230800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
18	chr9:2229800-2231600	Weak transcription	HSMM	muscle
19	chr9:2229800-2231600	Weak transcription	HSMMtube	muscle
20	chr9:2229800-2233800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:2229800-2234200	Weak transcription	HMEC	breast
22	chr9:2230000-2234800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:2230000-2241200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:2230200-2231400	Weak transcription	Fetal Heart	heart
25	chr9:2230200-2234400	Weak transcription	Right Ventricle	heart
26	chr9:2230200-2234600	Weak transcription	Right Atrium	heart
27	chr9:2230200-2241200	Weak transcription	Stomach Mucosa	stomach

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