Variant report

Variant	rs4608869
Chromosome Location	chr4:55098936-55098937
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	chr4:54795899..54796889-chr4:55098747..55099955,3	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11133315	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12505054	0.84[AFR][1000 genomes]
rs12505491	0.80[ASN][1000 genomes]
rs12506290	0.80[ASN][1000 genomes]
rs12508225	0.80[ASN][1000 genomes]
rs12641563	0.80[ASN][1000 genomes]
rs12644709	0.80[ASN][1000 genomes]
rs12644749	0.80[ASN][1000 genomes]
rs1565669	0.80[ASN][1000 genomes]
rs1565670	0.80[ASN][1000 genomes]
rs17084051	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800809	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800810	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1800812	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800813	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229307	0.80[ASN][1000 genomes]
rs2307049	0.80[ASN][1000 genomes]
rs28528897	0.80[ASN][1000 genomes]
rs28600756	0.80[ASN][1000 genomes]
rs4358459	0.80[ASN][1000 genomes]
rs4368668	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398585	0.86[AFR][1000 genomes]
rs4422471	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4635872	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864855	0.86[AFR][1000 genomes]
rs4864856	0.88[AFR][1000 genomes]
rs4864857	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864858	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864859	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864860	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864861	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864862	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864863	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864864	0.80[ASN][1000 genomes]
rs4864865	0.80[ASN][1000 genomes]
rs56145315	0.80[ASN][1000 genomes]
rs58435984	0.84[ASN][1000 genomes]
rs58727676	0.80[ASN][1000 genomes]
rs60806423	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60863210	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61320297	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554160	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67279506	0.80[ASN][1000 genomes]
rs67432867	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67600360	0.80[ASN][1000 genomes]
rs6831380	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6832597	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6836215	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6850748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73252942	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73252946	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73252948	0.80[ASN][1000 genomes]
rs7660560	0.80[ASN][1000 genomes]
rs7673027	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673267	0.82[AFR][1000 genomes]
rs7673597	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7673625	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673853	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7673984	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7676972	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7677751	0.94[ASN][1000 genomes]
rs7678144	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679903	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681399	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682912	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7683707	0.88[AFR][1000 genomes]
rs7686588	0.80[ASN][1000 genomes]
rs7688997	0.80[ASN][1000 genomes]
rs7689569	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690503	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7691129	0.80[ASN][1000 genomes]
rs7698425	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs890203	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991165	0.84[AMR][1000 genomes];0.85[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	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002905	chr4:55093677-55115698	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55091200-55099000	Bivalent/Poised TSS	Fetal Kidney	kidney
2	chr4:55092000-55100800	Active TSS	Aorta	Aorta
3	chr4:55092400-55100600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:55093200-55100800	Active TSS	NHDF-Ad	bronchial
5	chr4:55093200-55102000	Active TSS	Ovary	ovary
6	chr4:55094200-55099000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr4:55094200-55100800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:55094800-55100800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:55095000-55100400	Active TSS	Osteobl	bone
10	chr4:55095000-55100600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:55095000-55100800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr4:55095600-55099400	Bivalent/Poised TSS	Psoas Muscle	Psoas
13	chr4:55095600-55100600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr4:55096000-55100000	Bivalent/Poised TSS	Thymus	Thymus
15	chr4:55096000-55100600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr4:55096000-55100800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr4:55096200-55099000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
18	chr4:55096200-55099200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
19	chr4:55096200-55099400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr4:55096600-55099400	Bivalent/Poised TSS	Colonic Mucosa	Colon
21	chr4:55096600-55100600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr4:55096600-55100600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:55096600-55101400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:55096800-55099200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:55097000-55099200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:55097000-55099600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:55097000-55099600	Bivalent Enhancer	Fetal Brain Male	brain
28	chr4:55097200-55099000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
29	chr4:55097400-55099200	Active TSS	Gastric	stomach
30	chr4:55097400-55100600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr4:55097400-55101200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr4:55097600-55099000	Bivalent Enhancer	Stomach Mucosa	stomach
33	chr4:55097800-55099200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr4:55097800-55099200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
35	chr4:55097800-55099200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:55097800-55100400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:55098000-55099000	Flanking Bivalent TSS/Enh	HepG2	liver
38	chr4:55098000-55099200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:55098000-55099200	Bivalent/Poised TSS	Fetal Lung	lung
40	chr4:55098000-55100400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr4:55098000-55101000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr4:55098200-55099400	Active TSS	Lung	lung
43	chr4:55098200-55100200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:55098400-55099000	Bivalent Enhancer	Spleen	Spleen
45	chr4:55098400-55099200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:55098400-55099200	Active TSS	Right Ventricle	heart
47	chr4:55098400-55099600	Active TSS	NHLF	lung
48	chr4:55098400-55101200	Active TSS	Right Atrium	heart
49	chr4:55098400-55101400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:55098600-55099000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links