Variant report

Variant	rs6445222
Chromosome Location	chr3:61545571-61545572
allele	A/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	CTCF	chr3:61545460-61545610	HCPEpiC	choroid plexus:	n/a	n/a
2	KAP1	chr3:61545082-61545692	U2OS	brain:	n/a	n/a
3	BRCA1	chr3:61545545-61545576	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:61545459-61545861	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:61545334-61545823	SK-N-MC	brain:	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	TBP	chr3:61545558-61545786	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF263	chr3:61545560-61547635	HEK293-T-REx	kidney:	n/a	n/a
10	POLR2A	chr3:61545091-61547949	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:61545560-61545710	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61538544..61540472-chr3:61544545..61547220,2	K562	blood:

Variant related genes	Relation type
PTPRG	TF binding region

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1574016	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17669146	0.95[ASN][1000 genomes]
rs1878772	0.98[ASN][1000 genomes]
rs2886519	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6445221	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6445224	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7636186	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808938	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9821236	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9824541	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9827952	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9840322	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9845678	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61542200-61545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:61545000-61545600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:61545000-61545600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:61545000-61545600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:61545000-61545600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:61545000-61545600	Enhancers	Fetal Kidney	kidney
7	chr3:61545000-61545600	Enhancers	Fetal Muscle Leg	muscle
8	chr3:61545000-61545600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:61545000-61545600	Enhancers	NHDF-Ad	bronchial
10	chr3:61545000-61545800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:61545000-61545800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:61545000-61545800	Flanking Active TSS	Osteobl	bone
13	chr3:61545000-61546000	Enhancers	Fetal Heart	heart
14	chr3:61545000-61547800	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr3:61545000-61549600	Active TSS	NHEK	skin
16	chr3:61545000-61550800	Active TSS	Psoas Muscle	Psoas
17	chr3:61545200-61545600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
18	chr3:61545200-61545600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:61545200-61545600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
20	chr3:61545200-61545600	Enhancers	NH-A	brain
21	chr3:61545200-61545800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr3:61545200-61545800	Weak transcription	Right Atrium	heart
23	chr3:61545200-61545800	Flanking Active TSS	HepG2	liver
24	chr3:61545200-61549400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:61545400-61545600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
26	chr3:61545400-61545600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:61545400-61545600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:61545400-61545600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
29	chr3:61545400-61545600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:61545400-61545600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
31	chr3:61545400-61545600	Enhancers	Fetal Intestine Large	intestine
32	chr3:61545400-61545600	Flanking Active TSS	Placenta	Placenta
33	chr3:61545400-61545600	Enhancers	Fetal Stomach	stomach
34	chr3:61545400-61545600	Enhancers	Dnd41	blood
35	chr3:61545400-61545600	Flanking Active TSS	NHLF	lung
36	chr3:61545400-61545800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:61545400-61545800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:61545400-61545800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:61545400-61545800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr3:61545400-61545800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr3:61545400-61545800	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr3:61545400-61546000	Enhancers	Lung	lung
43	chr3:61545400-61546400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:61545400-61546400	Flanking Active TSS	HUVEC	blood vessel
45	chr3:61545400-61546600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr3:61545400-61549000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr3:61545400-61549600	Active TSS	Duodenum Mucosa	Duodenum
48	chr3:61545400-61550400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:61545400-61550800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr3:61545400-61550800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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