Variant report

Variant	rs1279424
Chromosome Location	chr3:136007333-136007334
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	chr3:135911672..135913999-chr3:136007331..136010292,2	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10935181	0.83[EUR][1000 genomes]
rs10935184	0.87[EUR][1000 genomes]
rs1153877	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11915629	0.81[EUR][1000 genomes]
rs12488721	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1279086	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1279949	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs480162	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs480330	0.85[ASN][1000 genomes]
rs517319	0.81[AMR][1000 genomes]
rs518972	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs527888	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs553018	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs556788	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56235965	0.81[EUR][1000 genomes]
rs570621	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589092	0.87[ASN][1000 genomes]
rs619605	0.83[AMR][1000 genomes]
rs650326	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs654237	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs655836	0.83[EUR][1000 genomes]
rs664088	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66691851	0.83[EUR][1000 genomes]
rs681783	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs684195	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs696081	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs696520	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs711972	0.81[EUR][1000 genomes]
rs73222302	0.82[EUR][1000 genomes]
rs838202	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1279424	PCCB	cis	multi-tissue	Pritchard
rs1279424	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135976200-136012400	Weak transcription	NHLF	lung
3	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
4	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:135981200-136052000	Weak transcription	NH-A	brain
6	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
7	chr3:135996800-136016000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:135997000-136010600	Weak transcription	Gastric	stomach
9	chr3:135997000-136012000	Weak transcription	Spleen	Spleen
10	chr3:135997400-136015200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:135999800-136013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:135999800-136013000	Weak transcription	Small Intestine	intestine
14	chr3:135999800-136016200	Weak transcription	Esophagus	oesophagus
15	chr3:135999800-136016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:135999800-136019000	Weak transcription	NHEK	skin
17	chr3:135999800-136038200	Weak transcription	Fetal Brain Male	brain
18	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
19	chr3:136000000-136016600	Weak transcription	Thymus	Thymus
20	chr3:136000000-136024600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:136000200-136008200	Strong transcription	Dnd41	blood
22	chr3:136000200-136012200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:136000200-136038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:136001200-136008200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:136001200-136011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:136001200-136016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:136001200-136019200	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:136001400-136008200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:136001600-136007600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:136001800-136007600	Strong transcription	Liver	Liver
31	chr3:136002000-136007600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:136002000-136007600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:136002000-136007800	Strong transcription	Fetal Stomach	stomach
34	chr3:136002000-136008000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:136002000-136017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:136002200-136008200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:136002200-136012400	Weak transcription	Brain Angular Gyrus	brain
38	chr3:136002200-136014800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:136002200-136015600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:136002400-136009400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:136002400-136010400	Weak transcription	Psoas Muscle	Psoas
42	chr3:136002400-136012000	Weak transcription	Pancreas	Pancrea
43	chr3:136002600-136007600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:136002600-136007600	Strong transcription	Adipose Nuclei	Adipose
45	chr3:136002600-136007600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:136002600-136010200	Weak transcription	Fetal Heart	heart
47	chr3:136002800-136012600	Weak transcription	GM12878-XiMat	blood
48	chr3:136003000-136012200	Weak transcription	Aorta	Aorta
49	chr3:136003000-136016400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:136004000-136007600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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