Variant report

Variant	rs1279949
Chromosome Location	chr3:135996870-135996871
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135914067..135916251-chr3:135996323..135999070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10935181	0.82[EUR][1000 genomes]
rs10935184	0.85[EUR][1000 genomes]
rs1153877	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488721	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1279086	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1279424	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3957816	0.83[ASN][1000 genomes]
rs480162	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs480330	0.89[ASN][1000 genomes]
rs518972	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527888	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553018	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556788	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56235965	0.80[EUR][1000 genomes]
rs570621	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589092	0.96[ASN][1000 genomes]
rs590198	0.83[ASN][1000 genomes]
rs632251	0.83[ASN][1000 genomes]
rs634559	0.83[ASN][1000 genomes]
rs650326	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs654237	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs655836	0.82[EUR][1000 genomes]
rs661739	0.83[ASN][1000 genomes]
rs664088	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66691851	0.81[EUR][1000 genomes]
rs668437	0.81[ASN][1000 genomes]
rs681783	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs684195	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs696081	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs696520	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs711972	0.80[EUR][1000 genomes]
rs73222302	0.81[EUR][1000 genomes]
rs838202	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs895894	0.83[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
rs1279949	PCCB	cis	multi-tissue	Pritchard
rs1279949	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-135998800	Weak transcription	Fetal Brain Male	brain
2	chr3:135970600-135999200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:135970600-135999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:135970800-135998000	Weak transcription	Hela-S3	cervix
6	chr3:135974800-135997800	Weak transcription	Stomach Mucosa	stomach
7	chr3:135976200-135999400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:135976200-136012400	Weak transcription	NHLF	lung
9	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
10	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:135980800-135997600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:135980800-135999200	Weak transcription	Small Intestine	intestine
13	chr3:135981000-135998600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:135981200-135999200	Weak transcription	NHDF-Ad	bronchial
15	chr3:135981200-136052000	Weak transcription	NH-A	brain
16	chr3:135981600-135997200	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:135981600-135998000	Weak transcription	Fetal Heart	heart
18	chr3:135981600-135998800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:135981600-136020400	Weak transcription	HUVEC	blood vessel
20	chr3:135981800-135999600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:135982600-135997800	Weak transcription	HSMMtube	muscle
22	chr3:135982600-135999000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:135982600-136004000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:135984600-135998000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:135984600-135998000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:135985600-135999400	Weak transcription	Osteobl	bone
27	chr3:135985800-135997600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:135986400-135998200	Weak transcription	A549	lung
29	chr3:135986800-135997600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:135987800-135998000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:135988000-135999200	Weak transcription	Thymus	Thymus
32	chr3:135988400-135997200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:135988600-135999000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:135990000-135997800	Weak transcription	GM12878-XiMat	blood
35	chr3:135993600-135998800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:135994000-135998200	Weak transcription	Fetal Kidney	kidney
37	chr3:135994800-135997400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr3:135995000-135997000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:135995000-135997200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:135995000-135997200	Enhancers	Psoas Muscle	Psoas
41	chr3:135995000-135997200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:135995000-135998600	Strong transcription	Liver	Liver
43	chr3:135995000-136000800	ZNF genes & repeats	Fetal Brain Female	brain
44	chr3:135995000-136001200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:135995200-135997000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:135995200-135997000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:135995200-135997200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:135995200-135997200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr3:135995200-135997200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:135995200-135997400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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