Variant report

Variant	rs721122
Chromosome Location	chr15:34379605-34379606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34378589..34383223-chr15:34392480..34394966,4	K562	blood:

Variant related genes	Relation type
ENSG00000134153	Chromatin interaction
ENSG00000182405	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11072954	0.89[EUR][1000 genomes]
rs11634597	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11853879	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856158	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs12592547	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs12592856	0.82[EUR][1000 genomes]
rs12594048	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs12903028	0.82[EUR][1000 genomes]
rs1436923	0.88[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16958770	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865925	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339374	0.82[EUR][1000 genomes]
rs2568532	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576310	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28376576	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794593	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288968	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4468578	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4780214	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4780215	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4780216	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522397	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs56310728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57205845	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs623941	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6495519	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161835	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7163226	0.93[EUR][1000 genomes]
rs7182085	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73374335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028703	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038259	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer 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 target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs721122	PGBD4	cis	cerebellum	SCAN
rs721122	PGBD4	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34358600-34393000	Weak transcription	Aorta	Aorta
2	chr15:34368000-34391600	Weak transcription	Right Ventricle	heart
3	chr15:34368800-34392400	Weak transcription	Psoas Muscle	Psoas
4	chr15:34369600-34391600	Weak transcription	NHEK	skin
5	chr15:34372800-34393200	Weak transcription	Colonic Mucosa	Colon
6	chr15:34373600-34392400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:34374200-34383800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:34374200-34392800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:34374400-34391600	Weak transcription	Fetal Brain Male	brain
10	chr15:34374600-34382600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr15:34374600-34382600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:34374800-34379800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:34374800-34380800	Weak transcription	Pancreas	Pancrea
14	chr15:34374800-34381000	Strong transcription	Fetal Thymus	thymus
15	chr15:34374800-34382000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:34374800-34382600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:34374800-34383000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:34374800-34384200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:34374800-34385600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:34374800-34391600	Weak transcription	Small Intestine	intestine
21	chr15:34374800-34393000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:34375000-34382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:34375000-34382800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:34375000-34386800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:34375000-34392800	Weak transcription	Fetal Heart	heart
26	chr15:34375000-34393000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:34375200-34380800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:34375200-34382600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:34375400-34381200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:34375400-34382600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:34375400-34382600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:34375400-34382600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:34375400-34382800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:34375400-34388800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:34375400-34388800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:34375600-34380400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:34375600-34380800	Strong transcription	Primary B cells from cord blood	blood
38	chr15:34375600-34380800	Strong transcription	Osteobl	bone
39	chr15:34375600-34381200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:34375600-34381600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:34375600-34381600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:34375600-34382200	Strong transcription	Placenta	Placenta
43	chr15:34375600-34382600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:34375600-34382600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:34375600-34382600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr15:34375600-34382800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:34375600-34382800	Strong transcription	Liver	Liver
48	chr15:34375600-34382800	Strong transcription	Fetal Intestine Large	intestine
49	chr15:34375600-34383000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:34375600-34389000	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links