Variant report

Variant	rs2119226
Chromosome Location	chr8:102952899-102952900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:102944466..102946820-chr8:102951965..102953968,2	MCF-7	breast:
2	chr8:102948704..102951699-chr8:102951896..102954688,2	K562	blood:
3	chr8:102952026..102954914-chr8:103250526..103252790,2	MCF-7	breast:
4	chr8:102952850..102955242-chr8:102955407..102957253,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246263	Chromatin interaction
ENSG00000048392	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10097554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10099842	0.89[CEU][hapmap]
rs1119377	0.89[CEU][hapmap]
rs11778653	0.92[CEU][hapmap]
rs12545403	0.92[CEU][hapmap]
rs1371740	0.89[CEU][hapmap]
rs1543771	0.89[CEU][hapmap]
rs17495818	0.92[CEU][hapmap]
rs1866691	0.85[CEU][hapmap]
rs2119225	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs2387332	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4145554	0.92[CEU][hapmap]
rs4734043	0.89[CEU][hapmap]
rs4734044	0.89[CEU][hapmap]
rs4734045	0.89[CEU][hapmap]
rs4734047	0.89[CEU][hapmap]
rs4734048	0.89[CEU][hapmap]
rs4734601	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4734602	0.85[CEU][hapmap]
rs4734603	0.89[CEU][hapmap]
rs4734606	0.89[CEU][hapmap]
rs479316	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs484507	0.89[ASN][1000 genomes]
rs516608	0.90[JPT][hapmap]
rs573618	0.89[ASN][1000 genomes]
rs6468803	0.92[CEU][hapmap]
rs6468804	0.88[CEU][hapmap]
rs6468805	0.88[CEU][hapmap]
rs6468807	0.89[CEU][hapmap]
rs6981347	0.89[CEU][hapmap]
rs6982001	0.85[CEU][hapmap]
rs6982161	0.85[GIH][hapmap]
rs6991019	0.92[CEU][hapmap]
rs6991178	0.92[CEU][hapmap]
rs6995105	0.89[CEU][hapmap]
rs6999316	0.89[CEU][hapmap]
rs7003289	0.91[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs7003320	0.88[CEU][hapmap]
rs7010848	0.92[CEU][hapmap]
rs7015981	0.92[CEU][hapmap]
rs718262	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs718263	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7820244	0.89[CEU][hapmap]
rs7820497	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs7823856	0.88[CEU][hapmap]
rs7838556	0.92[CEU][hapmap]
rs7839884	0.89[CEU][hapmap]
rs7840045	0.89[CEU][hapmap]
rs9297315	0.85[CEU][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9297316	0.89[ASN][1000 genomes]
rs993639	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs995584	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018653	chr8:102818271-103009082	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539700	chr8:102818271-103009082	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv831411	chr8:102937991-103108140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2119226	NCALD	cis	cerebellum	SCAN
rs2119226	NCALD	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102920600-102956600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr8:102944400-102953600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr8:102944400-102964000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr8:102948600-102955200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:102948600-102962600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:102951000-102961400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr8:102952000-102953600	Enhancers	Ovary	ovary
8	chr8:102952600-102953000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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