Variant report

Variant	rs454582
Chromosome Location	chr13:111217913-111217914
allele	A/C
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	ESR1	chr13:111217576-111217969	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr13:111217138-111218243	ECC-1	luminal epithelium:	n/a	chr13:111217322-111217332
3	CTCF	chr13:111217766-111217937	LNCaP	prostate:	n/a	chr13:111217844-111217852
4	CTCF	chr13:111217780-111217930	HEK293	kidney:	n/a	chr13:111217844-111217852
5	CTCF	chr13:111217820-111217970	GM12871	blood:	n/a	chr13:111217844-111217852
6	NFIC	chr13:111217405-111218235	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr13:111216927-111218090	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr13:111217820-111217970	GM12873	blood:	n/a	chr13:111217844-111217852
9	TCF7L2	chr13:111217728-111217914	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr13:111217860-111218010	HMEC	breast:	n/a	n/a
11	RAD21	chr13:111217610-111218065	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOXA1	chr13:111217724-111218075	ECC-1	luminal epithelium:	n/a	n/a
13	RFX5	chr13:111217678-111217939	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr13:111217711-111217947	IMR90	lung:	n/a	chr13:111217844-111217852
15	NR3C1	chr13:111217521-111217966	ECC-1	luminal epithelium:	n/a	n/a
16	TCF12	chr13:111217043-111218229	ECC-1	luminal epithelium:	n/a	chr13:111217322-111217332
17	CTCF	chr13:111217780-111217930	GM12873	blood:	n/a	chr13:111217844-111217852
18	ESR1	chr13:111217601-111217951	ECC-1	luminal epithelium:	n/a	n/a
19	ZNF143	chr13:111217721-111217959	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr13:111217800-111217950	HFF	foreskin:	n/a	chr13:111217844-111217852
21	EP300	chr13:111217457-111218039	ECC-1	luminal epithelium:	n/a	chr13:111217925-111217935
22	MAX	chr13:111216778-111218103	ECC-1	luminal epithelium:	n/a	chr13:111216837-111216847
23	CTCF	chr13:111217780-111217930	HMF	breast:	n/a	chr13:111217844-111217852
24	ESR1	chr13:111217526-111218053	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr13:111217714-111217986	K562	blood:	n/a	chr13:111217844-111217852
26	CTCF	chr13:111217780-111217930	GM12874	blood:	n/a	chr13:111217844-111217852
27	SMC3	chr13:111217797-111217923	HepG2	liver:	n/a	n/a
28	RAD21	chr13:111217706-111217993	H1-hESC	embryonic stem cell:	n/a	n/a
29	TEAD4	chr13:111217441-111218087	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr13:111217780-111217930	HRPEpiC	eye:	n/a	chr13:111217844-111217852
31	CTCF	chr13:111217787-111217950	GM12878	blood:	n/a	chr13:111217844-111217852
32	CTCF	chr13:111217820-111217970	HFF-Myc	foreskin:	n/a	chr13:111217844-111217852
33	CTCF	chr13:111217741-111218003	GM12878	blood:	n/a	chr13:111217844-111217852
34	CTCF	chr13:111217800-111217950	HA-sp	spinal cord:	n/a	chr13:111217844-111217852
35	FOXA1	chr13:111217835-111217991	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr13:111217747-111217970	Hela-S3	cervix:	n/a	chr13:111217844-111217852
37	CTCF	chr13:111217780-111217930	HCT-116	colon:	n/a	chr13:111217844-111217852
38	CTCF	chr13:111217780-111217930	BE2_C	brain:	n/a	chr13:111217844-111217852
39	NFIC	chr13:111217440-111218150	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr13:111217860-111218010	HCT-116	colon:	n/a	n/a
41	EP300	chr13:111216807-111218250	ECC-1	luminal epithelium:	n/a	chr13:111217925-111217935
42	SMC3	chr13:111217726-111217927	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr13:111217800-111217950	GM12875	blood:	n/a	chr13:111217844-111217852
44	CTCF	chr13:111217780-111217930	GM12878	blood:	n/a	chr13:111217844-111217852
45	CTCF	chr13:111217780-111217930	HBMEC	blood vessel:	n/a	chr13:111217844-111217852
46	CTCF	chr13:111217780-111217930	NHEK	skin:	n/a	chr13:111217844-111217852
47	CTCF	chr13:111217780-111217930	Caco-2	colon:	n/a	chr13:111217844-111217852
48	CTCF	chr13:111217800-111217950	GM12874	blood:	n/a	chr13:111217844-111217852
49	CTCF	chr13:111217780-111217930	AG04450	lung:	n/a	chr13:111217844-111217852
50	CTCF	chr13:111217820-111217970	GM06990	blood:	n/a	chr13:111217844-111217852

No.	Distal block	Cell Line	Cell type
1	chr13:111217228..111219179-chr13:111567056..111569002,2	MCF-7	breast:
2	chr13:111205877..111207739-chr13:111217049..111218978,2	K562	blood:
3	chr13:111217584..111220349-chr13:111248231..111250917,2	MCF-7	breast:

Variant related genes	Relation type
RAB20	TF binding region
ENSG00000088448	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2025656	0.81[EUR][1000 genomes]
rs392473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420176	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430147	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445740	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4506764	0.88[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs4771691	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9521841	0.81[EUR][1000 genomes]

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	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases
4	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' 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	216 gene(s)	inside rSNPs	diseases
6	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
7	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111214800-111218600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:111214800-111226400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:111215200-111220000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:111215400-111218200	Weak transcription	Psoas Muscle	Psoas
5	chr13:111215400-111221000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:111215600-111222600	Weak transcription	Ovary	ovary
7	chr13:111215800-111219800	Weak transcription	Placenta	Placenta
8	chr13:111215800-111220000	Weak transcription	Small Intestine	intestine
9	chr13:111215800-111220800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:111216000-111220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:111216000-111220000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr13:111216000-111220600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:111216000-111227800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:111216000-111227800	Weak transcription	Gastric	stomach
15	chr13:111216200-111219000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr13:111216200-111219800	Weak transcription	K562	blood
17	chr13:111216200-111220800	Weak transcription	Adipose Nuclei	Adipose
18	chr13:111216200-111221000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:111216200-111221600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr13:111216200-111223200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr13:111216200-111226400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr13:111216600-111218800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr13:111216600-111223000	Weak transcription	Fetal Intestine Small	intestine
24	chr13:111216800-111218000	Enhancers	Hela-S3	cervix
25	chr13:111217000-111218000	Enhancers	Fetal Kidney	kidney
26	chr13:111217200-111218000	Weak transcription	Fetal Stomach	stomach
27	chr13:111217200-111227600	Weak transcription	Spleen	Spleen
28	chr13:111217200-111227800	Weak transcription	Pancreas	Pancrea
29	chr13:111217400-111218800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr13:111217400-111221200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr13:111217400-111227400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:111217600-111218800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr13:111217600-111223400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr13:111217600-111224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr13:111217800-111218600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:111217800-111218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr13:111217800-111218600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr13:111217800-111220000	Weak transcription	Fetal Intestine Large	intestine
39	chr13:111217800-111221600	Weak transcription	Rectal Mucosa Donor 31	rectum

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