Variant report

Variant	rs4289498
Chromosome Location	chr4:55145432-55145433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55133319..55135360-chr4:55145191..55147587,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10003055	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10004857	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10010509	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10020847	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10021728	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10028020	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10032688	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1105825	0.81[ASN][1000 genomes]
rs11133317	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733839	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931555	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11935157	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11940889	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13147194	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1547904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1547905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228230	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276948	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307050	0.91[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs2412556	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412558	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28374326	0.88[AMR][1000 genomes]
rs28698464	0.81[ASN][1000 genomes]
rs28811736	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35597368	0.81[ASN][1000 genomes]
rs3690	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733540	0.89[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4864872	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864875	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864876	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55732997	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55784333	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60218083	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67388297	0.81[ASN][1000 genomes]
rs6855761	0.81[ASN][1000 genomes]
rs73252950	0.81[ASN][1000 genomes]
rs7677708	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9993187	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1004408	chr4:55124471-55179212	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 target site	1 gene(s)	inside rSNPs	diseases
4	nsv537099	chr4:55124471-55179212	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1001094	chr4:55131860-55189739	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55119400-55148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:55121000-55147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:55121000-55153200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:55121200-55147200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:55124400-55147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:55131600-55148000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:55136600-55148600	Strong transcription	Fetal Lung	lung
8	chr4:55137000-55145600	Strong transcription	Fetal Stomach	stomach
9	chr4:55137400-55161600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:55138200-55148400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:55139000-55153000	Weak transcription	Fetal Kidney	kidney
12	chr4:55139800-55148600	Genic enhancers	Osteobl	bone
13	chr4:55140000-55147200	Weak transcription	Esophagus	oesophagus
14	chr4:55140200-55149200	Weak transcription	Fetal Intestine Small	intestine
15	chr4:55140400-55149400	Genic enhancers	NHDF-Ad	bronchial
16	chr4:55140800-55148600	Genic enhancers	NHLF	lung
17	chr4:55141200-55149000	Weak transcription	Placenta	Placenta
18	chr4:55141600-55145600	Strong transcription	Fetal Muscle Leg	muscle
19	chr4:55141800-55147200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:55142000-55145600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:55142000-55148200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:55142800-55146800	Genic enhancers	Ovary	ovary
23	chr4:55143400-55147200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:55143400-55147200	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:55143600-55146000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:55143600-55147000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:55143600-55147200	Weak transcription	Psoas Muscle	Psoas
28	chr4:55143600-55148800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:55143600-55164600	Weak transcription	Colonic Mucosa	Colon
30	chr4:55143800-55147600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr4:55143800-55148000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:55143800-55149000	Weak transcription	Fetal Intestine Large	intestine
33	chr4:55143800-55149200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:55143800-55150400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:55144000-55146200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:55144000-55146600	Weak transcription	Adipose Nuclei	Adipose
37	chr4:55144200-55146600	Weak transcription	Stomach Mucosa	stomach
38	chr4:55144200-55147200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:55144200-55147200	Weak transcription	Right Ventricle	heart
40	chr4:55144200-55147200	Weak transcription	HMEC	breast
41	chr4:55144200-55147200	Weak transcription	HSMMtube	muscle
42	chr4:55144200-55147400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:55144400-55146600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:55144400-55146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:55144400-55147000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:55144400-55147000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:55144400-55147200	Weak transcription	Left Ventricle	heart
48	chr4:55144400-55147200	Weak transcription	HSMM	muscle
49	chr4:55144400-55147200	Weak transcription	NHEK	skin
50	chr4:55144400-55148400	Weak transcription	Spleen	Spleen

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