Variant report

Variant	rs17084716
Chromosome Location	chr4:55598706-55598707
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	chr4:55594122..55596921-chr4:55598697..55601658,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157404	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1124007	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11935331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17084694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17084702	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17084733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17084745	0.80[ASN][1000 genomes]
rs2237012	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2237014	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2276949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298976	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733542	0.83[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3796776	0.96[ASN][1000 genomes]
rs3822214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234238	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55561000-55606600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:55576400-55602000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:55576400-55602600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:55584400-55606200	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:55585200-55608400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:55586600-55604600	Weak transcription	Lung	lung
7	chr4:55587800-55607600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:55588200-55608000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:55588600-55611600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:55589600-55608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:55589800-55607400	Weak transcription	Left Ventricle	heart
12	chr4:55590000-55603400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:55590000-55608000	Strong transcription	Primary hematopoietic stem cells	blood
14	chr4:55590600-55602200	Weak transcription	Fetal Brain Female	brain
15	chr4:55591800-55599200	Weak transcription	Adipose Nuclei	Adipose
16	chr4:55592600-55609000	Weak transcription	Fetal Stomach	stomach
17	chr4:55593400-55607200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:55593600-55602600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:55593600-55606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:55593800-55600400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:55594200-55602200	Weak transcription	Aorta	Aorta
22	chr4:55594400-55602600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:55594400-55607000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:55594600-55599800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:55596200-55599800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr4:55596600-55598800	Weak transcription	Fetal Brain Male	brain
27	chr4:55597000-55600600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:55597400-55599600	Enhancers	Fetal Lung	lung
29	chr4:55597800-55603000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:55597800-55603200	Weak transcription	Ovary	ovary
31	chr4:55597800-55607600	Weak transcription	Fetal Kidney	kidney
32	chr4:55598000-55603200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:55598200-55599200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:55598200-55599400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:55598200-55600000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:55598200-55601600	Weak transcription	NHDF-Ad	bronchial
37	chr4:55598200-55607400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:55598400-55599000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links