Variant report

Variant	rs61957233
Chromosome Location	chr13:52702960-52702961
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	CTCF	chr13:52702870-52703639	HCT-116	colon:	n/a	n/a
2	SIN3AK20	chr13:52702842-52703305	HepG2	liver:	n/a	n/a
3	TCF12	chr13:52702896-52703468	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr13:52702945-52703510	MCF-7	breast:	n/a	n/a
5	EGR1	chr13:52702794-52703372	HCT-116	colon:	n/a	chr13:52703050-52703064 chr13:52703013-52703027
6	MXI1	chr13:52702955-52703519	H1-hESC	embryonic stem cell:	n/a	chr13:52702985-52703000 chr13:52702983-52702998
7	MYC	chr13:52702953-52703027	MCF-7	breast:	n/a	chr13:52702985-52702994
8	YY1	chr13:52702833-52703368	HepG2	liver:	n/a	n/a
9	RAD21	chr13:52702953-52703442	SK-N-SH_RA	brain:	n/a	n/a
10	ZBTB7A	chr13:52702367-52703532	ECC-1	luminal epithelium:	n/a	n/a
11	MYC	chr13:52702930-52703417	K562	blood:	n/a	chr13:52702985-52702994
12	RAD21	chr13:52702823-52703575	ECC-1	luminal epithelium:	n/a	n/a
13	MXI1	chr13:52702909-52703034	Hela-S3	cervix:	n/a	chr13:52702985-52703000 chr13:52702983-52702998
14	MAX	chr13:52702869-52703075	K562	blood:	n/a	chr13:52702985-52702994
15	EGR1	chr13:52702834-52703314	ECC-1	luminal epithelium:	n/a	chr13:52703050-52703064 chr13:52703013-52703027
16	EGR1	chr13:52702918-52703143	GM12878	blood:	n/a	chr13:52703050-52703064 chr13:52703013-52703027
17	SIN3A	chr13:52702686-52703073	GM12878	blood:	n/a	n/a
18	RAD21	chr13:52702960-52703504	H1-hESC	embryonic stem cell:	n/a	n/a
19	ELF1	chr13:52702759-52703453	GM12878	blood:	n/a	n/a
20	EGR1	chr13:52702833-52703346	K562	blood:	n/a	chr13:52703050-52703064 chr13:52703013-52703027
21	CTCF	chr13:52702920-52703070	AoAF	blood vessel:	n/a	n/a
22	MAX	chr13:52702918-52703505	MCF-7	breast:	n/a	chr13:52702985-52702994
23	MAX	chr13:52702795-52703495	H1-hESC	embryonic stem cell:	n/a	chr13:52702985-52702994
24	MAX	chr13:52702892-52703389	HepG2	liver:	n/a	chr13:52702985-52702994
25	SIN3AK20	chr13:52702693-52703425	H1-hESC	embryonic stem cell:	n/a	n/a
26	EGR1	chr13:52702848-52703291	K562	blood:	n/a	chr13:52703050-52703064 chr13:52703013-52703027
27	RAD21	chr13:52702866-52703440	IMR90	lung:	n/a	n/a
28	UBTF	chr13:52702960-52703404	K562	blood:	n/a	n/a
29	MAZ	chr13:52702510-52703468	K562	blood:	n/a	chr13:52702985-52702994
30	MAX	chr13:52701862-52703543	NB4	blood:	n/a	chr13:52702985-52702994
31	MAX	chr13:52702754-52703474	ECC-1	luminal epithelium:	n/a	chr13:52702985-52702994
32	EGR1	chr13:52702789-52703249	MCF-7	breast:	n/a	chr13:52703050-52703064 chr13:52703013-52703027
33	ELF1	chr13:52702894-52703317	K562	blood:	n/a	n/a
34	RCOR1	chr13:52702951-52703367	K562	blood:	n/a	n/a
35	MXI1	chr13:52701908-52703423	HepG2	liver:	n/a	chr13:52702985-52703000 chr13:52702983-52702998
36	MAX	chr13:52701670-52703501	ECC-1	luminal epithelium:	n/a	chr13:52702985-52702994
37	MAX	chr13:52702929-52703458	H1-hESC	embryonic stem cell:	n/a	chr13:52702985-52702994
38	CTCF	chr13:52702950-52702992	GM12891	blood:	n/a	n/a
39	RAD21	chr13:52702904-52703524	H1-hESC	embryonic stem cell:	n/a	n/a
40	EGR1	chr13:52702742-52703397	ECC-1	luminal epithelium:	n/a	chr13:52703050-52703064 chr13:52703013-52703027
41	MXI1	chr13:52702852-52703221	GM12878	blood:	n/a	chr13:52702985-52703000 chr13:52702983-52702998
42	POLR2A	chr13:52702749-52703464	ECC-1	luminal epithelium:	n/a	n/a
43	RAD21	chr13:52702803-52703579	HCT-116	colon:	n/a	n/a
44	CTCF	chr13:52702860-52703010	HA-sp	spinal cord:	n/a	n/a
45	MAX	chr13:52702828-52703407	K562	blood:	n/a	chr13:52702985-52702994
46	MAZ	chr13:52701717-52703491	IMR90	lung:	n/a	chr13:52702985-52702994
47	MXI1	chr13:52701549-52703476	IMR90	lung:	n/a	chr13:52702985-52703000 chr13:52702983-52702998
48	SIN3AK20	chr13:52702759-52703616	MCF-7	breast:	n/a	n/a
49	SIN3A	chr13:52701864-52703495	H1-hESC	embryonic stem cell:	n/a	n/a
50	RAD21	chr13:52701361-52703701	SK-N-SH	brain:	n/a	chr13:52702753-52702767 chr13:52702727-52702737

No.	Distal block	Cell Line	Cell type
1	chr13:52701771..52705558-chr13:52767896..52769871,3	MCF-7	breast:
2	chr13:52376169..52378547-chr13:52701514..52703656,2	MCF-7	breast:
3	chr13:52584477..52586943-chr13:52701489..52703372,3	K562	blood:
4	chr13:52377335..52378174-chr13:52702786..52703324,2	K562	blood:
5	chr13:52584477..52586900-chr13:52700506..52703372,3	K562	blood:

Variant related genes	Relation type
NEK5	TF binding region
ENSG00000123191	Chromatin interaction
ENSG00000243406	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000253710	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1122934	1.00[ASN][1000 genomes]
rs4091568	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4941729	1.00[ASN][1000 genomes]
rs55667430	0.87[ASN][1000 genomes]
rs55715265	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57345934	1.00[ASN][1000 genomes]
rs61957231	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957232	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957238	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957248	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957249	1.00[ASN][1000 genomes]
rs61957252	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957253	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957254	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61957255	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957256	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61957258	1.00[ASN][1000 genomes]
rs61957297	1.00[ASN][1000 genomes]
rs61958782	1.00[ASN][1000 genomes]
rs61958784	1.00[ASN][1000 genomes]
rs61958786	1.00[ASN][1000 genomes]
rs61958788	1.00[ASN][1000 genomes]
rs61958800	1.00[ASN][1000 genomes]
rs61958801	1.00[ASN][1000 genomes]
rs61958802	1.00[ASN][1000 genomes]
rs61958803	1.00[ASN][1000 genomes]
rs61958806	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61958807	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61958860	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61958863	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61958865	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs719349	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7333070	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73502305	1.00[ASN][1000 genomes]
rs73502307	1.00[ASN][1000 genomes]
rs9526818	1.00[ASN][1000 genomes]
rs9526840	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535814	1.00[ASN][1000 genomes]
rs9535818	1.00[ASN][1000 genomes]
rs9535831	1.00[ASN][1000 genomes]
rs9535838	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535839	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535850	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535852	1.00[ASN][1000 genomes]
rs9535859	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535869	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535870	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535875	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535881	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535886	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535890	1.00[ASN][1000 genomes]
rs9535892	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535893	1.00[ASN][1000 genomes]
rs9535894	1.00[ASN][1000 genomes]
rs9535897	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535900	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535901	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535902	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535903	1.00[ASN][1000 genomes]
rs9535906	1.00[ASN][1000 genomes]
rs9535909	1.00[ASN][1000 genomes]
rs9535910	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535911	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535913	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9536044	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52701800-52703000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr13:52701800-52703000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr13:52701800-52703000	Flanking Active TSS	NHEK	skin
4	chr13:52701800-52703000	Flanking Active TSS	Osteobl	bone
5	chr13:52701800-52703600	Active TSS	Aorta	Aorta
6	chr13:52701800-52703600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr13:52701800-52703600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr13:52702000-52703000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr13:52702000-52703000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr13:52702000-52703000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr13:52702000-52703000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr13:52702000-52703000	Flanking Active TSS	HUVEC	blood vessel
13	chr13:52702000-52703000	Flanking Active TSS	NH-A	brain
14	chr13:52702000-52703400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr13:52702000-52703400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:52702000-52703400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr13:52702000-52703400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:52702000-52703400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr13:52702000-52703400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
20	chr13:52702000-52703400	Active TSS	Brain Substantia Nigra	brain
21	chr13:52702000-52703400	Active TSS	Right Atrium	heart
22	chr13:52702000-52703400	Active TSS	Right Ventricle	heart
23	chr13:52702000-52703600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:52702000-52703600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:52702000-52703600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr13:52702000-52703600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr13:52702000-52703600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr13:52702000-52703600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
29	chr13:52702000-52703600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr13:52702000-52703600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:52702000-52703600	Flanking Active TSS	Liver	Liver
32	chr13:52702000-52703600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:52702000-52703600	Active TSS	Fetal Kidney	kidney
34	chr13:52702000-52703600	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr13:52702000-52703600	Active TSS	Psoas Muscle	Psoas
36	chr13:52702000-52703600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr13:52702000-52703600	Active TSS	A549	lung
38	chr13:52702000-52703600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr13:52702000-52703600	Active TSS	NHDF-Ad	bronchial
40	chr13:52702000-52703800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr13:52702000-52703800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr13:52702000-52703800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr13:52702000-52703800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr13:52702000-52703800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr13:52702000-52703800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:52702000-52703800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:52702000-52703800	Active TSS	Brain Anterior Caudate	brain
48	chr13:52702200-52703000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr13:52702200-52703000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr13:52702200-52703000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood

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