Variant report

Variant	rs72888645
Chromosome Location	chr3:61545205-61545206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr3:61545082-61545692	U2OS	brain:	n/a	n/a
2	CHD2	chr3:61545095-61545392	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAFK	chr3:61545020-61545220	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr3:61545060-61545210	HCT-116	colon:	n/a	n/a
5	POLR2A	chr3:61544738-61545491	HepG2	liver:	n/a	n/a
6	JUND	chr3:61545042-61545696	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:61544864-61554855	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr3:61545200-61545350	BJ	skin:	n/a	n/a
9	POLR2A	chr3:61545091-61547949	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFK	chr3:61545011-61545210	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61541363..61545409-chr3:61545583..61548750,5	MCF-7	breast:
2	chr3:61538544..61540472-chr3:61544545..61547220,2	K562	blood:

No data

Variant related genes	Relation type
PTPRG	TF binding region
ENSG00000144724	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs72888619	1.00[AMR][1000 genomes]
rs72888624	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72888626	1.00[AMR][1000 genomes]
rs72888639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72888649	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72888663	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv822105	chr3:61531517-61556259	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv1841066	chr3:61534766-61550452	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61542200-61545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:61543800-61545400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:61544600-61545400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:61544800-61545400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:61544800-61545400	Enhancers	Placenta	Placenta
6	chr3:61545000-61545400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:61545000-61545400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr3:61545000-61545400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:61545000-61545400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:61545000-61545400	Enhancers	Left Ventricle	heart
11	chr3:61545000-61545400	Enhancers	HUVEC	blood vessel
12	chr3:61545000-61545400	Enhancers	NHLF	lung
13	chr3:61545000-61545600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:61545000-61545600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:61545000-61545600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:61545000-61545600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:61545000-61545600	Enhancers	Fetal Kidney	kidney
18	chr3:61545000-61545600	Enhancers	Fetal Muscle Leg	muscle
19	chr3:61545000-61545600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:61545000-61545600	Enhancers	NHDF-Ad	bronchial
21	chr3:61545000-61545800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr3:61545000-61545800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:61545000-61545800	Flanking Active TSS	Osteobl	bone
24	chr3:61545000-61546000	Enhancers	Fetal Heart	heart
25	chr3:61545000-61547800	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr3:61545000-61549600	Active TSS	NHEK	skin
27	chr3:61545000-61550800	Active TSS	Psoas Muscle	Psoas
28	chr3:61545200-61545400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr3:61545200-61545400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr3:61545200-61545400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr3:61545200-61545400	Enhancers	Adipose Nuclei	Adipose
32	chr3:61545200-61545400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr3:61545200-61545600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
34	chr3:61545200-61545600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:61545200-61545600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
36	chr3:61545200-61545600	Enhancers	NH-A	brain
37	chr3:61545200-61545800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr3:61545200-61545800	Weak transcription	Right Atrium	heart
39	chr3:61545200-61545800	Flanking Active TSS	HepG2	liver
40	chr3:61545200-61549400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links