Variant report

Variant	rs711977
Chromosome Location	chr3:136227387-136227388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1070228	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11719310	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1394094	0.83[ASN][1000 genomes]
rs2688600	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688601	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4630889	0.82[AFR][1000 genomes]
rs4678269	0.86[AMR][1000 genomes]
rs711975	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73226190	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7427564	0.85[AFR][1000 genomes]
rs833861	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9714347	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs711977	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
3	chr3:136176600-136240000	Weak transcription	HMEC	breast
4	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
7	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:136193800-136231400	Weak transcription	NHLF	lung
11	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:136195200-136231000	Weak transcription	Osteobl	bone
13	chr3:136195400-136231400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:136195400-136232000	Weak transcription	Right Ventricle	heart
15	chr3:136195400-136241800	Weak transcription	NH-A	brain
16	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:136208400-136230400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:136210800-136229600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:136211600-136232000	Weak transcription	Fetal Kidney	kidney
21	chr3:136212200-136229200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:136212400-136231000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:136212400-136232000	Weak transcription	Aorta	Aorta
25	chr3:136212400-136241600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:136212400-136249600	Weak transcription	Lung	lung
27	chr3:136212600-136248200	Weak transcription	Esophagus	oesophagus
28	chr3:136213000-136231000	Weak transcription	Ovary	ovary
29	chr3:136213000-136239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:136213000-136251000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:136213000-136252200	Weak transcription	Left Ventricle	heart
32	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:136213200-136246000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:136213200-136246600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:136213400-136231000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:136214000-136239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:136214000-136246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:136214400-136238400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:136214600-136231000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:136215000-136230000	Weak transcription	Fetal Lung	lung
41	chr3:136215600-136246200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:136218400-136227400	Weak transcription	Fetal Stomach	stomach
43	chr3:136218400-136227600	Weak transcription	Thymus	Thymus
44	chr3:136218400-136235000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:136218600-136235600	Weak transcription	HUVEC	blood vessel
46	chr3:136219800-136231400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:136220600-136231200	Weak transcription	Adipose Nuclei	Adipose
48	chr3:136220600-136240000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:136220600-136242800	Weak transcription	GM12878-XiMat	blood
50	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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