Variant report

Variant	rs28650939
Chromosome Location	chr4:55133959-55133960
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	chr4:55133319..55135360-chr4:55145191..55147587,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10028020	0.85[EUR][1000 genomes]
rs1105825	0.86[EUR][1000 genomes]
rs12505491	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12506290	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12508225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12641563	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12644749	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565669	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565670	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2229307	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307049	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307050	0.86[EUR][1000 genomes]
rs28374326	0.86[EUR][1000 genomes]
rs28489067	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28528897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28600756	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35597368	0.85[EUR][1000 genomes]
rs4358459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864864	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864865	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56145315	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58435984	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58727676	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67279506	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67388297	0.86[EUR][1000 genomes]
rs67600360	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6855761	0.86[EUR][1000 genomes]
rs73252946	0.92[ASN][1000 genomes]
rs73252948	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73252950	0.83[EUR][1000 genomes]
rs7660560	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7686588	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7688997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7691129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9991165	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55119000-55138600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:55119400-55148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:55121000-55147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:55121000-55153200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:55121200-55147200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:55122400-55142600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:55124400-55140400	Weak transcription	Placenta	Placenta
8	chr4:55124400-55147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:55124800-55134000	Weak transcription	Fetal Brain Male	brain
10	chr4:55124800-55138600	Weak transcription	NH-A	brain
11	chr4:55125400-55140600	Strong transcription	Ovary	ovary
12	chr4:55125800-55135800	Strong transcription	Fetal Lung	lung
13	chr4:55126400-55140800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:55126600-55134400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:55127000-55138600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:55127200-55135600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:55127800-55140600	Weak transcription	Left Ventricle	heart
18	chr4:55129200-55139000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:55129200-55142400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:55129800-55136000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:55130000-55135400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:55130000-55139000	Weak transcription	Esophagus	oesophagus
23	chr4:55130000-55139000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:55130200-55142800	Weak transcription	Gastric	stomach
25	chr4:55130200-55143000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:55130400-55134200	Strong transcription	Fetal Kidney	kidney
27	chr4:55130600-55142400	Weak transcription	Right Ventricle	heart
28	chr4:55131600-55148000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:55131800-55134200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:55131800-55137200	Weak transcription	Spleen	Spleen
31	chr4:55132000-55134200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:55132200-55142200	Weak transcription	Liver	Liver
33	chr4:55132400-55134200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:55132400-55142800	Weak transcription	Adipose Nuclei	Adipose
35	chr4:55132600-55134000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:55133000-55135600	Strong transcription	Aorta	Aorta
37	chr4:55133200-55134200	Strong transcription	NHLF	lung
38	chr4:55133200-55143200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr4:55133400-55134000	Enhancers	Psoas Muscle	Psoas
40	chr4:55133400-55134000	Enhancers	HUVEC	blood vessel
41	chr4:55133400-55134200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:55133400-55135200	Strong transcription	Fetal Intestine Large	intestine
43	chr4:55133400-55135400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:55133400-55135400	Strong transcription	Fetal Stomach	stomach
45	chr4:55133400-55135600	Strong transcription	Fetal Muscle Leg	muscle
46	chr4:55133400-55135600	Genic enhancers	NHDF-Ad	bronchial
47	chr4:55133400-55135600	Genic enhancers	Osteobl	bone
48	chr4:55133400-55143000	Weak transcription	Colonic Mucosa	Colon
49	chr4:55133600-55135600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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