Variant report

Variant	rs702720
Chromosome Location	chr5:57757383-57757384
allele	A/C/G/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	RAD21	chr5:57754174-57757575	SK-N-SH	brain:	n/a	chr5:57755497-57755509 chr5:57756736-57756755 chr5:57755955-57755967 chr5:57755364-57755374 chr5:57756324-57756337 chr5:57756780-57756792 chr5:57756742-57756751
2	CHD1	chr5:57751128-57757458	IMR90	lung:	n/a	n/a
3	CTCF	chr5:57754818-57757550	A549	lung:	n/a	chr5:57756239-57756248 chr5:57756739-57756755 chr5:57756740-57756753 chr5:57756238-57756251 chr5:57756235-57756248 chr5:57756738-57756756 chr5:57756733-57756754
4	SETDB1	chr5:57756581-57757391	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:57068006..57070437-chr5:57756613..57758535,2	MCF-7	breast:
2	chr17:56707798..56710603-chr5:57755406..57757452,2	MCF-7	breast:
3	chr5:57364074..57376813-chr5:57753679..57758569,26	MCF-7	breast:
4	chr1:11968161..11969978-chr5:57755723..57757847,2	MCF-7	breast:
5	chr5:57754652..57757569-chr8:146051207..146054086,2	MCF-7	breast:
6	chr5:57158588..57161134-chr5:57757060..57758676,2	MCF-7	breast:

Variant related genes	Relation type
PLK2	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000147789	Chromatin interaction
ENSG00000238899	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10051454	1.00[AFR][1000 genomes]
rs10057291	0.83[AFR][1000 genomes]
rs10065306	0.83[AFR][1000 genomes]
rs10070159	0.83[AFR][1000 genomes]
rs10940616	0.83[AFR][1000 genomes]
rs13173334	1.00[AFR][1000 genomes]
rs13174658	0.83[AFR][1000 genomes]
rs13184329	1.00[AFR][1000 genomes]
rs150249	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs150271	0.94[ASN][1000 genomes]
rs151890	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs151893	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs154472	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs154474	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs154491	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs154492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154493	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs158154	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158158	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158159	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158280	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158281	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17773723	0.83[AFR][1000 genomes]
rs17773753	0.83[AFR][1000 genomes]
rs32613	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs32614	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs39967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42739	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs42740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67873319	0.83[AFR][1000 genomes]
rs697134	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702709	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs702710	0.97[ASN][1000 genomes]
rs702717	0.97[ASN][1000 genomes]
rs702721	1.00[ASN][1000 genomes]
rs702723	0.82[JPT][hapmap]
rs832631	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs832636	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3437453	chr5:57755020-57757568	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57756800-57757800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:57756800-57757800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:57756800-57757800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:57756800-57757800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:57756800-57757800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:57756800-57758000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:57756800-57758000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:57756800-57758000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:57756800-57758000	Enhancers	Fetal Intestine Large	intestine
10	chr5:57756800-57758000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:57756800-57758000	Enhancers	HepG2	liver
12	chr5:57756800-57758400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:57756800-57758600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr5:57756800-57758600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr5:57756800-57758600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:57756800-57758600	Enhancers	Dnd41	blood
17	chr5:57756800-57758600	Enhancers	HUVEC	blood vessel
18	chr5:57756800-57759200	Weak transcription	Small Intestine	intestine
19	chr5:57756800-57762800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:57756800-57762800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:57757000-57757400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:57757000-57757400	Enhancers	NH-A	brain
23	chr5:57757000-57757600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:57757000-57757600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:57757000-57757600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:57757000-57757800	Enhancers	Liver	Liver
27	chr5:57757000-57757800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr5:57757000-57758000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:57757000-57758000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:57757000-57758000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr5:57757000-57758000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:57757000-57758000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:57757000-57758000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:57757000-57758000	Weak transcription	Placenta	Placenta
35	chr5:57757000-57758000	Weak transcription	HSMM	muscle
36	chr5:57757000-57758000	Weak transcription	HSMMtube	muscle
37	chr5:57757000-57758000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:57757000-57758000	Weak transcription	NHDF-Ad	bronchial
39	chr5:57757000-57758000	Weak transcription	NHLF	lung
40	chr5:57757000-57758000	Weak transcription	Osteobl	bone
41	chr5:57757000-57758200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:57757000-57758200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:57757000-57758200	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:57757000-57758200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:57757000-57758200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr5:57757000-57758200	Weak transcription	Stomach Mucosa	stomach
47	chr5:57757000-57758400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr5:57757000-57758400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:57757000-57758400	Weak transcription	Brain Anterior Caudate	brain
50	chr5:57757000-57758400	Weak transcription	Brain Substantia Nigra	brain

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