Variant report

Variant	rs16844362
Chromosome Location	chr3:136704008-136704009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:136703553-136704028	Hela-S3	cervix:	n/a	n/a
2	FOS	chr3:136703718-136704114	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr3:136703602-136704039	Hela-S3	cervix:	n/a	chr3:136703988-136703997
4	FOS	chr3:136703708-136704147	MCF10A-Er-Src	breast:	n/a	n/a
5	GTF2F1	chr3:136703602-136704044	Hela-S3	cervix:	n/a	n/a
6	EP300	chr3:136703429-136704072	Hela-S3	cervix:	n/a	chr3:136703937-136703951 chr3:136703539-136703548
7	STAT3	chr3:136703720-136704113	MCF10A-Er-Src	breast:	n/a	chr3:136703892-136703904
8	MAX	chr3:136703517-136704160	Hela-S3	cervix:	n/a	chr3:136703988-136703997
9	TCF7L2	chr3:136703548-136704063	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr3:136703429-136704138	Hela-S3	cervix:	n/a	n/a
11	RFX5	chr3:136703602-136704093	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:136703826-136704176	Hela-S3	cervix:	n/a	n/a
13	RCOR1	chr3:136703526-136704158	IMR90	lung:	n/a	n/a
14	CHD2	chr3:136703601-136704028	Hela-S3	cervix:	n/a	n/a
15	SMC3	chr3:136703437-136704036	Hela-S3	cervix:	n/a	n/a
16	MAX	chr3:136703654-136704028	Hela-S3	cervix:	n/a	chr3:136703988-136703997
17	BRCA1	chr3:136703429-136704107	Hela-S3	cervix:	n/a	n/a
18	MAZ	chr3:136703429-136704066	Hela-S3	cervix:	n/a	chr3:136703988-136703997
19	MYC	chr3:136703662-136704112	MCF10A-Er-Src	breast:	n/a	chr3:136703988-136703997
20	STAT3	chr3:136703807-136704087	MCF10A-Er-Src	breast:	n/a	chr3:136703892-136703904
21	FOS	chr3:136703823-136704088	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr3:136703659-136704152	MCF10A-Er-Src	breast:	n/a	n/a
23	MXI1	chr3:136703429-136704112	Hela-S3	cervix:	n/a	n/a
24	STAT3	chr3:136703681-136704145	MCF10A-Er-Src	breast:	n/a	chr3:136703892-136703904
25	STAT3	chr3:136703724-136704064	MCF10A-Er-Src	breast:	n/a	chr3:136703892-136703904
26	POLR2A	chr3:136703733-136704051	K562	blood:	n/a	n/a
27	FOS	chr3:136703735-136704109	MCF10A-Er-Src	breast:	n/a	n/a
28	TFAP2C	chr3:136703597-136704159	Hela-S3	cervix:	n/a	n/a
29	TBP	chr3:136703429-136704074	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr3:136703655-136704160	Hela-S3	cervix:	n/a	n/a
31	CEBPB	chr3:136703825-136704148	IMR90	lung:	n/a	n/a
32	MYC	chr3:136703706-136704088	MCF10A-Er-Src	breast:	n/a	chr3:136703988-136703997
33	USF2	chr3:136703598-136704078	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136697313..136700260-chr3:136703197..136704911,2	MCF-7	breast:

Variant related genes	Relation type
IL20RB-AS1	TF binding region
ENSG00000174564	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10935213	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935214	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1097288	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12054218	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054219	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12054408	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12494558	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1624703	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1654904	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654923	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654925	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654926	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1682333	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1682337	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1682356	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1682357	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16844325	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16844326	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168635	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163896	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35289288	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs361237	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361239	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361241	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361242	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361243	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs361244	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361245	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361246	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361248	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs361250	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs361251	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361252	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747842	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747843	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs75976	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs75977	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835632	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835633	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835634	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs835641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16844362	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136695400-136706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:136699800-136705400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:136701000-136704800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:136701600-136705200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:136702000-136705600	Enhancers	Fetal Thymus	thymus
6	chr3:136702200-136705600	Enhancers	Thymus	Thymus
7	chr3:136703000-136704600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:136703000-136704600	Enhancers	HSMM	muscle
9	chr3:136703000-136704800	Enhancers	HMEC	breast
10	chr3:136703200-136704200	Enhancers	Placenta	Placenta
11	chr3:136703200-136704400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:136703200-136704800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:136703400-136704200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:136703400-136704200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:136703400-136704200	Enhancers	Fetal Heart	heart
16	chr3:136703400-136704200	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr3:136703400-136704200	Enhancers	Small Intestine	intestine
18	chr3:136703400-136704800	Enhancers	Fetal Intestine Large	intestine
19	chr3:136703600-136704200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:136703600-136704200	Enhancers	Primary T cells from cord blood	blood
21	chr3:136703600-136704200	Flanking Active TSS	Hela-S3	cervix
22	chr3:136703600-136704400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:136703600-136704400	Enhancers	Fetal Muscle Leg	muscle
24	chr3:136703600-136704600	Enhancers	Fetal Intestine Small	intestine
25	chr3:136703600-136704600	Transcr. at gene 5' and 3'	NHEK	skin
26	chr3:136703600-136705000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:136703800-136704200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:136703800-136704200	Flanking Active TSS	HSMMtube	muscle
29	chr3:136703800-136706400	Weak transcription	Esophagus	oesophagus
30	chr3:136703800-136706600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:136703800-136706600	Weak transcription	Lung	lung
32	chr3:136703800-136708400	Weak transcription	Colonic Mucosa	Colon
33	chr3:136703800-136708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:136703800-136713600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:136703800-136732400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:136704000-136706400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:136704000-136708800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:136704000-136713200	Weak transcription	Right Atrium	heart
39	chr3:136704000-136713400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:136704000-136713400	Weak transcription	Pancreas	Pancrea
41	chr3:136704000-136714600	Weak transcription	Right Ventricle	heart
42	chr3:136704000-136730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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