Variant report

Variant	rs2948088
Chromosome Location	chr3:20099658-20099659
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	chr3:20081053..20084896-chr3:20098793..20102867,5	K562	blood:
2	chr3:20079576..20083677-chr3:20098793..20102064,4	K562	blood:

Variant related genes	Relation type
ENSG00000114166	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11128936	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11714203	0.87[ASN][1000 genomes]
rs2293139	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2365793	0.82[AMR][1000 genomes]
rs2623075	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929399	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929400	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929403	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2929405	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2948083	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2948086	1.00[EUR][1000 genomes]
rs2948087	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59213344	0.86[ASN][1000 genomes]
rs60355368	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784715	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs939851	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20086200-20102800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:20090800-20100600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:20095600-20099800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr3:20095600-20100000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:20095600-20100200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:20095600-20100200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:20095600-20100400	Enhancers	Fetal Heart	heart
8	chr3:20095600-20100800	Enhancers	Placenta	Placenta
9	chr3:20095800-20099800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:20095800-20099800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:20095800-20099800	Enhancers	Fetal Muscle Leg	muscle
12	chr3:20095800-20099800	Enhancers	Spleen	Spleen
13	chr3:20095800-20099800	Enhancers	HUVEC	blood vessel
14	chr3:20095800-20100400	Enhancers	Fetal Lung	lung
15	chr3:20095800-20100400	Enhancers	Psoas Muscle	Psoas
16	chr3:20095800-20100600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:20096000-20100200	Enhancers	Small Intestine	intestine
18	chr3:20096000-20100800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:20096600-20106400	Weak transcription	Fetal Intestine Large	intestine
20	chr3:20096800-20100600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:20096800-20102600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:20097000-20100400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr3:20097200-20100200	Enhancers	Brain Hippocampus Middle	brain
24	chr3:20097200-20104600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:20097200-20106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:20097400-20102400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:20097600-20099800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:20097600-20100400	Enhancers	Brain Anterior Caudate	brain
29	chr3:20098000-20099800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:20098000-20100000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:20098200-20099800	Enhancers	Left Ventricle	heart
32	chr3:20098200-20099800	Enhancers	Right Atrium	heart
33	chr3:20098200-20100200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr3:20098400-20099800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:20098400-20102200	Weak transcription	Primary T cells from cord blood	blood
36	chr3:20098600-20101800	Weak transcription	Primary B cells from cord blood	blood
37	chr3:20098800-20100200	Enhancers	NHEK	skin
38	chr3:20098800-20100400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr3:20098800-20100400	Enhancers	Thymus	Thymus
40	chr3:20098800-20102400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:20099000-20101400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:20099000-20102400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:20099000-20122600	Weak transcription	Aorta	Aorta
44	chr3:20099200-20100000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:20099200-20100000	Enhancers	Fetal Muscle Trunk	muscle
46	chr3:20099200-20102600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:20099200-20106000	Weak transcription	Right Ventricle	heart
48	chr3:20099400-20100800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:20099400-20101400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:20099400-20101600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links