Variant report

Variant	rs7003289
Chromosome Location	chr8:102951136-102951137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10097554	0.86[JPT][hapmap];0.93[YRI][hapmap];0.87[ASN][1000 genomes]
rs10505016	1.00[ASW][hapmap]
rs2119225	0.84[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2119226	0.91[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2387332	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4734051	1.00[ASW][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap]
rs4734601	0.99[ASN][1000 genomes]
rs479316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs484507	1.00[ASN][1000 genomes]
rs516608	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs573618	1.00[ASN][1000 genomes]
rs6982161	0.83[GIH][hapmap]
rs718262	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs718263	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7820497	0.82[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9297315	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs9297316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs993639	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs995584	0.88[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7003289	NCALD	cis	cerebellum	SCAN

Chromatin state (count:10 , 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	chr8:102944600-102952000	Weak transcription	Ovary	ovary
5	chr8:102945000-102952600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:102948600-102955200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:102948600-102962600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:102950400-102951200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr8:102951000-102952800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:102951000-102961400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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