Variant report

Variant	rs17084745
Chromosome Location	chr4:55607844-55607845
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55605484..55608271-chr4:55609162..55610751,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1124007	0.83[CEU][hapmap];0.95[GIH][hapmap]
rs11935331	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs17084694	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs17084702	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs17084716	0.80[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs17084733	0.80[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs2237012	0.83[CEU][hapmap];0.95[GIH][hapmap]
rs2276949	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2298976	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs3733542	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3796776	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822214	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs73234238	0.80[ASN][1000 genomes]
rs8022	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.84[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	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
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55585200-55608400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:55588200-55608000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:55588600-55611600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:55589600-55608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:55590000-55608000	Strong transcription	Primary hematopoietic stem cells	blood
6	chr4:55592600-55609000	Weak transcription	Fetal Stomach	stomach
7	chr4:55600000-55610000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:55601000-55616000	Weak transcription	Gastric	stomach
9	chr4:55603600-55609200	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:55604000-55608200	Weak transcription	Fetal Brain Female	brain
11	chr4:55604800-55608600	Weak transcription	Lung	lung
12	chr4:55604800-55613200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:55605000-55618400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:55605800-55612400	Weak transcription	NHDF-Ad	bronchial
15	chr4:55606000-55608400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:55606200-55608200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:55606200-55608800	Enhancers	Brain Hippocampus Middle	brain
18	chr4:55606200-55609600	Weak transcription	Aorta	Aorta
19	chr4:55606200-55611000	Weak transcription	Ovary	ovary
20	chr4:55606600-55608400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:55606800-55608000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:55606800-55608400	Enhancers	Brain Anterior Caudate	brain
23	chr4:55607000-55608000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:55607000-55608400	Enhancers	Brain Substantia Nigra	brain
25	chr4:55607000-55608600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:55607000-55608800	Enhancers	Brain Cingulate Gyrus	brain
27	chr4:55607000-55609200	Enhancers	H9 Cell Line	embryonic stem cell
28	chr4:55607400-55608000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:55607400-55609000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:55607600-55608000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr4:55607600-55608400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:55607600-55608400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:55607800-55608200	Enhancers	Brain Angular Gyrus	brain
34	chr4:55607800-55609000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:55607800-55609000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links