Variant report

Variant	rs1534164
Chromosome Location	chr3:133535082-133535083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133534001..133536701-chr3:133644896..133646543,2	K562	blood:
2	chr3:133529916..133531777-chr3:133534655..133536799,2	K562	blood:
3	chr3:133533795..133535800-chr3:133538596..133541212,2	K562	blood:
4	chr3:133533757..133536015-chr3:133537201..133540775,3	MCF-7	breast:
5	chr3:133534500..133536189-chr3:133546223..133548378,2	K562	blood:

Variant related genes	Relation type
ENSG00000144867	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2715631	0.81[LWK][hapmap]
rs6439441	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439442	0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs6439443	0.94[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs7650925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]

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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1534164	PCCB	cis	parietal	SCAN
rs1534164	SRPRB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133525400-133539000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:133525600-133538400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:133525600-133539000	Weak transcription	Gastric	stomach
4	chr3:133525600-133539200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:133525600-133541000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:133525800-133536400	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:133525800-133538800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:133525800-133538800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:133525800-133538800	Weak transcription	Stomach Mucosa	stomach
10	chr3:133525800-133541000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:133526200-133537400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:133526200-133540600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:133526200-133543400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:133526400-133536800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:133526400-133537200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:133526400-133537400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:133526400-133540200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:133526400-133543800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:133526400-133544000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:133526400-133544000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:133526600-133536200	Strong transcription	HSMM	muscle
22	chr3:133526600-133536800	Strong transcription	Fetal Muscle Leg	muscle
23	chr3:133526600-133537000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:133526600-133537000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:133526600-133537000	Strong transcription	Placenta	Placenta
26	chr3:133526600-133537200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:133526600-133537600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:133526600-133538000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:133526600-133539800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:133526600-133539800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:133526600-133543400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:133526600-133544800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr3:133526600-133544800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:133526800-133536600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:133526800-133537200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:133526800-133537200	Strong transcription	HUVEC	blood vessel
37	chr3:133526800-133537600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:133526800-133538400	Weak transcription	Small Intestine	intestine
39	chr3:133526800-133542000	Strong transcription	NH-A	brain
40	chr3:133526800-133544000	Strong transcription	Liver	Liver
41	chr3:133526800-133544800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr3:133527000-133541400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:133527000-133545000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:133527200-133545000	Strong transcription	Dnd41	blood
45	chr3:133527400-133537800	Strong transcription	NHEK	skin
46	chr3:133527800-133535800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:133527800-133537400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:133528000-133537400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr3:133528000-133543400	Strong transcription	Fetal Thymus	thymus
50	chr3:133528200-133537000	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links