Variant report

Variant	rs4630889
Chromosome Location	chr3:136278251-136278252
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	chr3:136277326..136280102-chr3:136471685..136473348,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1017882	0.88[AMR][1000 genomes]
rs1070228	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10935185	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935186	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11719310	0.82[AMR][1000 genomes]
rs11919030	0.90[AMR][1000 genomes]
rs12163529	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2688600	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688601	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34438032	0.88[AMR][1000 genomes]
rs4038587	0.85[AMR][1000 genomes]
rs4408829	0.82[AMR][1000 genomes]
rs4521165	0.88[AMR][1000 genomes]
rs4678269	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4678436	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55970317	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6439649	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66691851	0.82[EUR][1000 genomes]
rs6791142	0.87[AMR][1000 genomes]
rs6808312	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs711975	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs711977	0.82[AFR][1000 genomes]
rs73226190	0.81[AMR][1000 genomes]
rs73228043	0.90[AMR][1000 genomes]
rs7427564	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7432375	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7618518	0.88[AMR][1000 genomes]
rs7618871	0.82[AMR][1000 genomes]
rs7621308	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7637129	0.81[AMR][1000 genomes]
rs833861	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs940174	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9714347	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4630889	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs4630889	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 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	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:136246600-136286200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
8	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:136251600-136284400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:136251600-136284400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:136251600-136289400	Weak transcription	Adipose Nuclei	Adipose
13	chr3:136251600-136322400	Weak transcription	Liver	Liver
14	chr3:136251800-136284800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:136252600-136284800	Weak transcription	Left Ventricle	heart
16	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:136255200-136294000	Weak transcription	Primary T cells from cord blood	blood
20	chr3:136255800-136291600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:136257600-136282800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:136265000-136294200	Weak transcription	Fetal Lung	lung
24	chr3:136265200-136278600	Weak transcription	Brain Substantia Nigra	brain
25	chr3:136265400-136314800	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:136265800-136278400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:136266400-136315600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:136266600-136284200	Weak transcription	Primary B cells from cord blood	blood
29	chr3:136266600-136284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:136266600-136284800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:136266600-136291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:136266600-136314600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:136266600-136316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:136266800-136281600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:136266800-136284600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:136266800-136291000	Weak transcription	Hela-S3	cervix
37	chr3:136266800-136291800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:136266800-136314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:136267000-136278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:136267000-136297800	Weak transcription	HUVEC	blood vessel
41	chr3:136267200-136284800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:136268000-136289400	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
44	chr3:136268400-136284600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:136268600-136292400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:136268800-136285000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:136269000-136303200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:136269600-136295800	Weak transcription	Fetal Heart	heart
49	chr3:136270200-136279600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:136270400-136291600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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