Variant report

Variant	rs12505220
Chromosome Location	chr4:735974-735975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:735971-736765	K562	blood:	n/a	n/a
2	POLR2A	chr4:735969-737091	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:735522-737165	K562	blood:	n/a	n/a
4	POLR2A	chr4:735754-736808	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr4:735808-736831	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:734991..736577-chr4:768033..771031,2	K562	blood:
2	chr4:717561..720117-chr4:734344..736075,2	K562	blood:
3	chr4:735917..738355-chr4:773628..776647,3	MCF-7	breast:
4	chr4:726284..729928-chr4:730296..736157,5	MCF-7	breast:
5	chr4:678244..681266-chr4:735203..738855,3	MCF-7	breast:
6	chr4:735724..738302-chr4:774438..777111,2	MCF-7	breast:

No data

Variant related genes	Relation type
PCGF3	TF binding region
ENSG00000248416	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000169026	Chromatin interaction
ENSG00000249592	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10004172	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11248035	0.81[ASN][1000 genomes]
rs11248036	0.81[ASN][1000 genomes]
rs11728488	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11735280	0.89[ASN][1000 genomes]
rs12374317	0.81[ASN][1000 genomes]
rs12374324	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12502944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504026	0.81[ASN][1000 genomes]
rs17164964	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690189	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690192	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690294	0.88[ASN][1000 genomes]
rs4690295	0.88[ASN][1000 genomes]
rs55990625	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845891	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73221121	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73221124	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73221200	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
6	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	104 gene(s)	inside rSNPs	diseases
10	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
11	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv593209	chr4:686563-747810	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv1833383	chr4:708887-753697	Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv878253	chr4:708932-771587	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
15	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv878256	chr4:712222-744098	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
20	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
21	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
22	nsv4195	chr4:727187-768059	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12505220	PCGF3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:702200-754800	Weak transcription	Hela-S3	cervix
2	chr4:708200-736400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:715600-750200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:720000-738400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:720800-738400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:721000-738600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:721000-743600	Weak transcription	Right Atrium	heart
8	chr4:722000-736000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:723600-736400	Strong transcription	Fetal Brain Female	brain
10	chr4:723600-738600	Strong transcription	Brain Germinal Matrix	brain
11	chr4:723800-736200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:723800-737600	Strong transcription	Dnd41	blood
13	chr4:723800-738400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:724200-738600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:724200-738600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:724600-736400	Strong transcription	Fetal Lung	lung
17	chr4:724600-736600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:725200-738400	Strong transcription	Thymus	Thymus
19	chr4:725200-738600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:725200-738600	Strong transcription	Fetal Stomach	stomach
21	chr4:725800-738400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:725800-738600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:726200-736400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:726200-738400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:726200-738400	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr4:726200-738600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:726800-736400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:727000-767600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr4:727200-738200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:727600-736400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:728000-741800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:728600-755800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:728600-763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:729000-742400	Weak transcription	Small Intestine	intestine
35	chr4:729000-754600	Weak transcription	Fetal Kidney	kidney
36	chr4:729000-762600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:729600-753800	Weak transcription	Psoas Muscle	Psoas
38	chr4:729600-760800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:729800-738400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:729800-741600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:732000-737400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:732000-742400	Weak transcription	NHDF-Ad	bronchial
43	chr4:732000-745200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:732200-741800	Weak transcription	K562	blood
45	chr4:732200-743600	Weak transcription	HMEC	breast
46	chr4:733400-738400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:733600-737200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:733600-738400	Strong transcription	Fetal Intestine Small	intestine
49	chr4:733600-741600	Weak transcription	Brain Angular Gyrus	brain
50	chr4:733600-741600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links