Variant report

Variant	rs1923875
Chromosome Location	chr13:52376486-52376487
allele	C/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	MAX	chr13:52376308-52376639	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr13:52376027-52376769	Hela-S3	cervix:	n/a	n/a
3	BATF	chr13:52376333-52376661	GM12878	blood:	n/a	n/a
4	RUNX3	chr13:52376219-52376718	GM12878	blood:	n/a	n/a
5	POLR2A	chr13:52376417-52379808	GM12878	blood:	n/a	n/a
6	POLR2A	chr13:52376455-52376609	HepG2	liver:	n/a	n/a
7	RCOR1	chr13:52375542-52376866	IMR90	lung:	n/a	n/a
8	CEBPB	chr13:52376355-52376699	Hela-S3	cervix:	n/a	n/a
9	EBF1	chr13:52376326-52376608	GM12878	blood:	n/a	n/a
10	EP300	chr13:52376358-52376635	Hela-S3	cervix:	n/a	n/a
11	NR3C1	chr13:52376283-52376690	A549	lung:	n/a	chr13:52376555-52376572 chr13:52376546-52376555
12	RUNX3	chr13:52376286-52376648	GM12878	blood:	n/a	n/a
13	FOS	chr13:52376331-52376677	MCF10A-Er-Src	breast:	n/a	n/a
14	PAX5	chr13:52376264-52376701	GM12878	blood:	n/a	n/a
15	CEBPB	chr13:52376328-52376654	IMR90	lung:	n/a	n/a
16	FOS	chr13:52376303-52376721	MCF10A-Er-Src	breast:	n/a	n/a
17	CHD2	chr13:52376411-52376668	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr13:52376283-52380704	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr13:52376252-52376681	SK-N-SH	brain:	n/a	n/a
20	STAT3	chr13:52376426-52376737	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr13:52375841-52380503	MCF10A-Er-Src	breast:	n/a	n/a
22	MXI1	chr13:52376388-52376649	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr13:52376044-52376637	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr13:52376277-52376796	HUVEC	blood vessel:	n/a	n/a
25	FOS	chr13:52376287-52376726	MCF10A-Er-Src	breast:	n/a	n/a
26	PBX3	chr13:52376179-52376790	SK-N-SH	brain:	n/a	n/a
27	ZNF143	chr13:52376382-52376547	Hela-S3	cervix:	n/a	n/a
28	TCF12	chr13:52376027-52376858	SK-N-SH	brain:	n/a	chr13:52376041-52376050
29	EBF1	chr13:52376190-52376656	GM12878	blood:	n/a	n/a
30	EP300	chr13:52376366-52376645	GM12878	blood:	n/a	n/a
31	IKZF1	chr13:52376352-52376672	GM12878	blood:	n/a	n/a
32	PBX3	chr13:52376172-52376704	SK-N-SH	brain:	n/a	n/a
33	RELA	chr13:52376328-52376913	GM18951	blood:	n/a	n/a
34	SMC3	chr13:52376377-52376707	Hela-S3	cervix:	n/a	n/a
35	STAT3	chr13:52376352-52376691	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr13:52376333-52376636	HCT-116	colon:	n/a	n/a
37	BATF	chr13:52376365-52376687	GM12878	blood:	n/a	n/a
38	FOS	chr13:52376296-52376770	HUVEC	blood vessel:	n/a	n/a
39	MYC	chr13:52376336-52376668	MCF10A-Er-Src	breast:	n/a	n/a
40	NR2F2	chr13:52375884-52376697	MCF-7	breast:	n/a	n/a
41	MAFK	chr13:52376336-52376626	HepG2	liver:	n/a	chr13:52376433-52376448
42	FOS	chr13:52376287-52376755	MCF10A-Er-Src	breast:	n/a	n/a
43	EBF1	chr13:52376292-52376680	GM12878	blood:	n/a	n/a
44	IRF4	chr13:52376273-52376721	GM12878	blood:	n/a	n/a
45	POLR2A	chr13:52375976-52376711	Hela-S3	cervix:	n/a	n/a
46	MAFK	chr13:52376341-52376627	HepG2	liver:	n/a	chr13:52376433-52376448
47	NR3C1	chr13:52376336-52376743	A549	lung:	n/a	chr13:52376555-52376572 chr13:52376546-52376555
48	STAT3	chr13:52376354-52376697	MCF10A-Er-Src	breast:	n/a	n/a
49	MYC	chr13:52376352-52376679	MCF10A-Er-Src	breast:	n/a	n/a
50	ESRRA	chr13:52375899-52379115	GM12878	blood:	n/a	chr13:52376359-52376371 chr13:52376363-52376381 chr13:52376361-52376371 chr13:52376359-52376375

No.	Distal block	Cell Line	Cell type
1	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
2	chr13:52022728..52028464-chr13:52376436..52381467,17	K562	blood:
3	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
4	chr13:52157329..52158871-chr13:52376423..52379239,3	K562	blood:
5	chr13:52376169..52378547-chr13:52701514..52703656,2	MCF-7	breast:
6	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
7	chr13:52015156..52017204-chr13:52376088..52377740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231856	TF binding region
ENSG00000139668	Chromatin interaction
ENSG00000197168	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000224892	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12856726	1.00[ASW][hapmap]
rs1543525	0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[ASN][1000 genomes]
rs492869	0.84[CHB][hapmap]
rs9535762	0.85[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs9535763	0.85[CHB][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs9535765	0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9535767	0.82[ASW][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs9634846	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv1840020	chr13:52345838-52388765	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52368200-52377000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr13:52370200-52376600	Weak transcription	Primary B cells from cord blood	blood
3	chr13:52372000-52377000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:52372200-52377400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:52373200-52377400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:52373400-52376600	Enhancers	Ovary	ovary
7	chr13:52373400-52377000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr13:52373600-52377400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:52374000-52377000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:52374000-52377200	Enhancers	Fetal Muscle Leg	muscle
11	chr13:52374000-52377400	Enhancers	Primary hematopoietic stem cells	blood
12	chr13:52374000-52377400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr13:52374200-52377000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr13:52374400-52376600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:52374400-52377000	Enhancers	Liver	Liver
16	chr13:52374400-52377000	Enhancers	Colon Smooth Muscle	Colon
17	chr13:52374400-52377000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr13:52374400-52377000	Enhancers	HepG2	liver
19	chr13:52374400-52377200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr13:52374400-52377200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr13:52374600-52376600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:52374600-52376600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:52374600-52376800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:52374600-52377000	Enhancers	Brain Hippocampus Middle	brain
25	chr13:52374600-52377200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:52374600-52377200	Enhancers	Brain Angular Gyrus	brain
27	chr13:52374600-52377200	Enhancers	Brain Cingulate Gyrus	brain
28	chr13:52374600-52377400	Enhancers	Placenta	Placenta
29	chr13:52374600-52377400	Enhancers	Psoas Muscle	Psoas
30	chr13:52374600-52377600	Enhancers	Lung	lung
31	chr13:52374800-52376600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:52375000-52376800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr13:52375000-52376800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:52375000-52377000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:52375000-52377200	Enhancers	Duodenum Mucosa	Duodenum
36	chr13:52375000-52377400	Enhancers	Right Atrium	heart
37	chr13:52375200-52376800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr13:52375400-52376600	Enhancers	Stomach Mucosa	stomach
39	chr13:52375400-52377000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr13:52375400-52377400	Enhancers	Pancreas	Pancrea
41	chr13:52375400-52377400	Enhancers	HUVEC	blood vessel
42	chr13:52375600-52376600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr13:52375600-52376600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr13:52375600-52376600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr13:52375600-52376800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr13:52375600-52376800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr13:52375600-52376800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr13:52375600-52376800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr13:52375600-52377000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr13:52375600-52377000	Enhancers	Duodenum Smooth Muscle	Duodenum

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