Variant report

Variant	rs11006959
Chromosome Location	chr10:28544786-28544787
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:28543012..28546500-chr10:28550223..28554148,7	MCF-7	breast:
2	chr10:28538163..28546243-chr10:28589319..28594336,15	MCF-7	breast:
3	chr10:28542577..28545073-chr10:28590628..28593089,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10763654	0.93[ASN][1000 genomes]
rs10763655	0.85[ASN][1000 genomes]
rs10763658	0.80[ASN][1000 genomes]
rs10826402	0.82[JPT][hapmap]
rs10826433	0.92[ASN][1000 genomes]
rs10826435	0.93[ASN][1000 genomes]
rs10826436	0.91[ASN][1000 genomes]
rs11006946	0.93[ASN][1000 genomes]
rs11006950	0.85[ASN][1000 genomes]
rs11006956	0.93[ASN][1000 genomes]
rs11006957	0.93[ASN][1000 genomes]
rs11006962	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006965	0.93[ASN][1000 genomes]
rs11006970	0.93[ASN][1000 genomes]
rs1418757	0.83[ASN][1000 genomes]
rs1418759	0.84[ASN][1000 genomes]
rs17758855	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870097	0.93[ASN][1000 genomes]
rs1870098	0.93[ASN][1000 genomes]
rs1953322	0.91[ASN][1000 genomes]
rs1953324	0.99[ASN][1000 genomes]
rs2085471	0.93[ASN][1000 genomes]
rs2100615	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2100616	0.93[ASN][1000 genomes]
rs2290701	0.83[ASN][1000 genomes]
rs61845911	0.93[ASN][1000 genomes]
rs6481515	0.83[ASN][1000 genomes]
rs7072480	0.93[ASN][1000 genomes]
rs7088465	0.83[ASN][1000 genomes]
rs9919516	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28519000-28552000	Weak transcription	Fetal Stomach	stomach
2	chr10:28535800-28551600	Weak transcription	Fetal Intestine Small	intestine
3	chr10:28537400-28552600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:28537600-28549400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr10:28537600-28552600	Weak transcription	Primary T cells from cord blood	blood
6	chr10:28537800-28550200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr10:28542000-28549400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:28542400-28552400	Weak transcription	Psoas Muscle	Psoas
9	chr10:28542800-28550200	Weak transcription	Aorta	Aorta
10	chr10:28543200-28545000	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr10:28543800-28545000	Enhancers	Colon Smooth Muscle	Colon
12	chr10:28543800-28545800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:28543800-28546400	Enhancers	HMEC	breast
14	chr10:28543800-28549200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr10:28544000-28545400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:28544000-28545600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr10:28544000-28545800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:28544000-28545800	Weak transcription	NH-A	brain
19	chr10:28544000-28545800	Enhancers	NHEK	skin
20	chr10:28544000-28546200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:28544000-28549400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:28544000-28552200	Weak transcription	Fetal Heart	heart
23	chr10:28544000-28555600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:28544200-28545800	Weak transcription	Osteobl	bone
25	chr10:28544200-28550000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:28544200-28552400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr10:28544200-28554600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr10:28544600-28544800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr10:28544600-28545200	Weak transcription	Left Ventricle	heart
30	chr10:28544600-28550200	Weak transcription	Pancreas	Pancrea

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