Variant report

Variant	rs4928240
Chromosome Location	chr3:99772415-99772416
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99762380..99765452-chr3:99771776..99774107,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12494994	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496041	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1387649	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1565341	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4928236	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414382	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440991	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777622	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778589	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73859922	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7431827	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7610759	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634628	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641782	0.85[EUR][1000 genomes]
rs7652706	0.85[EUR][1000 genomes]
rs9824430	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9827744	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872339	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][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

No data

Chromatin state (count:37 , 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	chr3:99762000-99778200	Weak transcription	Ovary	ovary
4	chr3:99765000-99772800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:99767000-99777000	Weak transcription	Aorta	Aorta
6	chr3:99767400-99773400	Weak transcription	Esophagus	oesophagus
7	chr3:99767400-99775000	Weak transcription	Psoas Muscle	Psoas
8	chr3:99767400-99779600	Weak transcription	Left Ventricle	heart
9	chr3:99767600-99772800	Weak transcription	Adipose Nuclei	Adipose
10	chr3:99767600-99779400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:99767600-99801000	Weak transcription	HSMM	muscle
12	chr3:99767800-99774800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:99767800-99777000	Weak transcription	HMEC	breast
14	chr3:99768200-99780400	Weak transcription	GM12878-XiMat	blood
15	chr3:99768400-99788000	Weak transcription	Primary B cells from cord blood	blood
16	chr3:99769000-99776400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:99770800-99787600	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:99771200-99775000	Enhancers	Fetal Intestine Large	intestine
19	chr3:99771200-99775000	Enhancers	Fetal Intestine Small	intestine
20	chr3:99771600-99778400	Weak transcription	K562	blood
21	chr3:99772000-99773200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:99772000-99773400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:99772200-99772600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:99772200-99773200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:99772200-99773400	Enhancers	HepG2	liver
26	chr3:99772200-99773600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:99772200-99773600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:99772200-99774000	Enhancers	Stomach Mucosa	stomach
29	chr3:99772200-99776400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:99772400-99772600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:99772400-99773200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:99772400-99773200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr3:99772400-99773400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:99772400-99773400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:99772400-99773400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:99772400-99773800	Enhancers	Duodenum Mucosa	Duodenum
37	chr3:99772400-99777400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links