Variant report

Variant	rs9979353
Chromosome Location	chr21:40798555-40798556
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40798389..40799917-chr21:40801424..40804136,2	K562	blood:
2	chr21:40797216..40799492-chr21:40822971..40825535,2	MCF-7	breast:
3	chr21:40758499..40762376-chr21:40796781..40799288,3	K562	blood:
4	chr21:40798110..40799717-chr21:40814722..40817598,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157578	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12483547	0.82[ASN][1000 genomes]
rs13050837	0.82[ASN][1000 genomes]
rs13051054	0.82[ASN][1000 genomes]
rs2049823	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2837010	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837011	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2837012	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2837013	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837014	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2837016	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2837027	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837028	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837033	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2837038	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4816626	0.85[ASN][1000 genomes]
rs4816628	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7276842	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7277602	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs8130381	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs9979289	0.86[JPT][hapmap]
rs9983100	0.85[ASN][1000 genomes]
rs9983180	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9983404	0.82[ASN][1000 genomes]
rs9983435	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs9983716	0.82[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	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9979353	LINC00114	cis	Artery Tibial	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40764600-40800600	Weak transcription	Psoas Muscle	Psoas
2	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
3	chr21:40778400-40816600	Weak transcription	Left Ventricle	heart
4	chr21:40779200-40801400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:40780400-40802200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:40780600-40801800	Weak transcription	Lung	lung
7	chr21:40781200-40798600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr21:40781200-40811000	Weak transcription	Aorta	Aorta
9	chr21:40781200-40813000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr21:40781200-40813200	Weak transcription	HSMMtube	muscle
11	chr21:40781400-40802000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr21:40785000-40800600	Weak transcription	Gastric	stomach
13	chr21:40794600-40802000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:40794800-40800800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr21:40794800-40801400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:40795000-40802000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr21:40795000-40802000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr21:40795200-40801400	Weak transcription	Right Atrium	heart
19	chr21:40795400-40798800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr21:40797200-40800200	Weak transcription	K562	blood

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