Variant report

Variant	rs17284017
Chromosome Location	chr7:26583720-26583721
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26576661..26579431-chr7:26581573..26583872,2	MCF-7	breast:
2	chr7:26582972..26584768-chr7:26586705..26589472,2	K562	blood:

Variant related genes	Relation type
ENSG00000122548	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1076284	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs12537002	0.80[ASN][1000 genomes]
rs12700746	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs13243495	0.93[ASN][1000 genomes]
rs17153874	0.93[ASN][1000 genomes]
rs17283843	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2190186	0.86[JPT][hapmap]
rs2391284	0.90[ASW][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs34066752	0.93[ASN][1000 genomes]
rs35496114	0.93[ASN][1000 genomes]
rs3757656	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4289709	0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4719871	0.80[ASN][1000 genomes]
rs6943220	0.93[ASN][1000 genomes]
rs6957136	0.80[ASN][1000 genomes]
rs6957786	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6968080	0.80[ASN][1000 genomes]
rs71521773	0.93[ASN][1000 genomes]
rs71521774	0.93[ASN][1000 genomes]
rs73063761	0.80[ASN][1000 genomes]
rs73063794	0.80[ASN][1000 genomes]
rs757804	0.82[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17284017	GGCT	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26578800-26591600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr7:26579400-26589000	Weak transcription	Fetal Thymus	thymus
3	chr7:26581800-26585200	Enhancers	Fetal Stomach	stomach
4	chr7:26582400-26586800	Enhancers	Fetal Muscle Leg	muscle
5	chr7:26582400-26592200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:26582600-26585000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:26583000-26584400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:26583200-26583800	Flanking Active TSS	Fetal Lung	lung
9	chr7:26583200-26585000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:26583400-26583800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr7:26583400-26584000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:26583400-26586800	Enhancers	Fetal Kidney	kidney
13	chr7:26583600-26584200	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links