Variant report

Variant	rs1997596
Chromosome Location	chr21:16578448-16578449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:16534393..16538479-chr21:16576836..16579884,4	MCF-7	breast:
2	chr21:16577448..16580419-chr21:16741231..16743015,2	MCF-7	breast:
3	chr21:16577077..16584288-chr21:16662087..16667374,8	MCF-7	breast:
4	chr21:16543825..16546494-chr21:16577749..16579512,2	MCF-7	breast:
5	chr21:16575011..16578774-chr21:16661740..16665186,4	MCF-7	breast:
6	chr21:16429926..16439498-chr21:16561851..16585948,113	MCF-7	breast:
7	chr21:16495374..16497178-chr21:16575873..16578741,2	MCF-7	breast:
8	chr21:16421751..16443998-chr21:16557859..16589610,273	MCF-7	breast:
9	chr21:16576908..16578947-chr21:16816097..16818886,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236471	Chromatin interaction
ENSG00000180530	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1997595	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823138	0.83[LWK][hapmap]
rs2823139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2823140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56038390	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv913413	chr21:16537728-16621859	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1997596	SAMSN1	cis	parietal	SCAN
rs1997596	TSSC4	trans	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16575400-16579600	Enhancers	HepG2	liver
2	chr21:16576200-16585600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr21:16576400-16580000	Enhancers	Adipose Nuclei	Adipose
4	chr21:16576800-16580400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:16577000-16581000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr21:16577200-16578600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr21:16577400-16580800	Weak transcription	Pancreas	Pancrea
8	chr21:16577400-16581200	Weak transcription	A549	lung
9	chr21:16577600-16578600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:16577600-16578800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr21:16577600-16579600	Weak transcription	Hela-S3	cervix
12	chr21:16577600-16584000	Weak transcription	Right Ventricle	heart
13	chr21:16577800-16578800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr21:16577800-16581200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr21:16577800-16581800	Weak transcription	Fetal Kidney	kidney
16	chr21:16577800-16582200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr21:16577800-16582600	Weak transcription	Right Atrium	heart
18	chr21:16578000-16579600	Enhancers	Liver	Liver
19	chr21:16578200-16579800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr21:16578200-16582600	Weak transcription	Left Ventricle	heart
21	chr21:16578400-16579200	Enhancers	GM12878-XiMat	blood
22	chr21:16578400-16583800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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