Variant report

Variant	rs281366
Chromosome Location	chr17:19800394-19800395
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	chr17:19769802..19772027-chr17:19799780..19804333,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKAP10-2	chr17:19800339-19800600	ENSG00000270091.1
2	lnc-AKAP10-2	chr17:19799903-19800583	ENSG00000270091.1

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16960545	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs281367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581607	1.00[ASN][1000 genomes]
rs6587211	1.00[ASN][1000 genomes]
rs7215639	1.00[ASN][1000 genomes]
rs7215769	1.00[ASN][1000 genomes]
rs7217928	1.00[ASN][1000 genomes]
rs7218251	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7219487	1.00[ASN][1000 genomes]
rs7224713	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8068015	1.00[ASN][1000 genomes]
rs8071670	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9890105	1.00[ASN][1000 genomes]
rs9892271	1.00[ASN][1000 genomes]
rs9895556	1.00[ASN][1000 genomes]
rs9896641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9897430	1.00[ASN][1000 genomes]
rs9900510	1.00[ASN][1000 genomes]
rs9912184	1.00[ASN][1000 genomes]
rs9913858	1.00[ASN][1000 genomes]
rs9914502	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv518888	chr17:19789453-19804247	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19794800-19800800	Weak transcription	Spleen	Spleen
2	chr17:19796400-19809800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19797600-19800400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:19797600-19800600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:19797800-19800400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr17:19798000-19800400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:19798200-19800800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:19798400-19804000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:19799200-19808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:19799400-19803800	Weak transcription	Thymus	Thymus
11	chr17:19799400-19805000	Weak transcription	Fetal Intestine Large	intestine
12	chr17:19799600-19800600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr17:19799600-19803800	Weak transcription	Primary T cells from cord blood	blood
14	chr17:19799800-19805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:19799800-19806800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr17:19799800-19807000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:19800000-19800400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:19800000-19800800	Enhancers	Liver	Liver
19	chr17:19800000-19801600	Enhancers	Fetal Heart	heart
20	chr17:19800000-19802200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:19800200-19800400	Weak transcription	NHLF	lung
22	chr17:19800200-19801600	Enhancers	Colon Smooth Muscle	Colon
23	chr17:19800200-19802000	Enhancers	A549	lung
24	chr17:19800200-19802200	Flanking Active TSS	Hela-S3	cervix
25	chr17:19800200-19802200	Enhancers	HSMMtube	muscle
26	chr17:19800200-19804000	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links