Variant report

Variant	rs4678269
Chromosome Location	chr3:136189865-136189866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1070228	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10804640	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10935183	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10935184	0.83[AMR][1000 genomes]
rs10935185	0.81[AMR][1000 genomes]
rs11717954	0.81[EUR][1000 genomes]
rs11719310	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12492510	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2688600	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688601	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4630889	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs655748	0.83[EUR][1000 genomes]
rs66691851	0.87[AMR][1000 genomes]
rs6791611	0.80[AMR][1000 genomes]
rs696518	0.83[EUR][1000 genomes]
rs711975	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs711977	0.86[AMR][1000 genomes]
rs73226190	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7427564	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs833861	0.89[AMR][1000 genomes]
rs834304	0.81[EUR][1000 genomes]
rs834305	0.82[EUR][1000 genomes]
rs864437	0.80[EUR][1000 genomes]
rs866758	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9714347	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4678269	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136190600	Weak transcription	Gastric	stomach
2	chr3:136176400-136194200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:136176400-136194400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:136176400-136194400	Weak transcription	HSMM	muscle
5	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:136176600-136190400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:136176600-136195000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:136176600-136195000	Weak transcription	Spleen	Spleen
9	chr3:136176600-136196600	Weak transcription	HUVEC	blood vessel
10	chr3:136176600-136212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
15	chr3:136176600-136240000	Weak transcription	HMEC	breast
16	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:136176800-136190000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:136176800-136190600	Weak transcription	Left Ventricle	heart
19	chr3:136176800-136190600	Weak transcription	Pancreas	Pancrea
20	chr3:136176800-136191600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:136176800-136193400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:136176800-136193400	Weak transcription	Esophagus	oesophagus
23	chr3:136176800-136193600	Weak transcription	Ovary	ovary
24	chr3:136176800-136194400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:136176800-136194400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:136176800-136194800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:136176800-136205800	Weak transcription	Small Intestine	intestine
28	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
30	chr3:136177000-136190400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:136177000-136191800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:136177400-136190200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:136177400-136190600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:136177400-136191600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:136177400-136198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:136177600-136193400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:136177800-136190800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:136177800-136191600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:136178000-136194600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:136178000-136212000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:136178400-136193400	Weak transcription	Fetal Brain Female	brain
43	chr3:136178400-136208200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:136178600-136192200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:136178600-136194400	Weak transcription	Brain Angular Gyrus	brain
46	chr3:136178600-136220200	Weak transcription	Fetal Brain Male	brain
47	chr3:136179000-136192400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:136179400-136204000	Weak transcription	Fetal Intestine Small	intestine
49	chr3:136179800-136190600	Weak transcription	Fetal Stomach	stomach
50	chr3:136179800-136212000	Weak transcription	Fetal Heart	heart

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