Variant report

Variant	rs4928151
Chromosome Location	chr3:99767553-99767554
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99721792..99723539-chr3:99765840..99767973,2	MCF-7	breast:
2	chr3:99757965..99760484-chr3:99766104..99767644,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10222474	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11719468	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs12488245	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1384062	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1387647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16841874	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1718235	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs2130369	0.88[CEU][hapmap]
rs35422475	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4928150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4928153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928230	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs4928235	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767441	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6798114	0.84[CEU][hapmap]
rs6802817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808765	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7619512	0.80[ASN][1000 genomes]
rs7629487	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7636776	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7649349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs766778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs793443	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs793446	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs793464	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs793502	0.83[CEU][hapmap];0.94[JPT][hapmap]
rs796976	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs813218	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs902159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289981	0.84[CEU][hapmap]
rs9811920	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9814549	0.84[CEU][hapmap]
rs9837131	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9849632	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4928151	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99752200-99774600	Weak transcription	Gastric	stomach
3	chr3:99759200-99768200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:99762000-99767600	Enhancers	HSMM	muscle
5	chr3:99762000-99778200	Weak transcription	Ovary	ovary
6	chr3:99763000-99767600	Enhancers	NHLF	lung
7	chr3:99764400-99767600	Enhancers	Fetal Muscle Leg	muscle
8	chr3:99764600-99767600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:99764600-99767600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:99764600-99767800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:99764600-99768600	Enhancers	Fetal Intestine Large	intestine
12	chr3:99764600-99769000	Enhancers	Fetal Intestine Small	intestine
13	chr3:99765000-99772800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:99765800-99767600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:99765800-99771800	Weak transcription	Hela-S3	cervix
16	chr3:99766200-99767600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:99766400-99767600	Flanking Active TSS	GM12878-XiMat	blood
18	chr3:99766800-99767800	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:99767000-99767600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:99767000-99767600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:99767000-99767600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:99767000-99767600	Enhancers	Adipose Nuclei	Adipose
23	chr3:99767000-99767600	Enhancers	Duodenum Mucosa	Duodenum
24	chr3:99767000-99767600	Enhancers	HepG2	liver
25	chr3:99767000-99767600	Enhancers	HSMMtube	muscle
26	chr3:99767000-99767800	Enhancers	HMEC	breast
27	chr3:99767000-99772000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:99767000-99772200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:99767000-99772400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:99767000-99772400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:99767000-99777000	Weak transcription	Aorta	Aorta
32	chr3:99767200-99768400	Enhancers	Primary B cells from cord blood	blood
33	chr3:99767400-99767600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:99767400-99767600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr3:99767400-99767800	Enhancers	NHEK	skin
36	chr3:99767400-99769000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:99767400-99772200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:99767400-99772200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:99767400-99772200	Weak transcription	Stomach Mucosa	stomach
40	chr3:99767400-99772400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:99767400-99773400	Weak transcription	Esophagus	oesophagus
42	chr3:99767400-99775000	Weak transcription	Psoas Muscle	Psoas
43	chr3:99767400-99779600	Weak transcription	Left Ventricle	heart

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