Variant report

Variant	rs321969
Chromosome Location	chr7:78313673-78313674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10485912	0.86[CEU][hapmap]
rs1859935	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs321964	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs321965	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs321967	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs321970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321995	0.97[EUR][1000 genomes]
rs321996	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs453795	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv888509	chr7:78307944-78327299	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs321969	SEMA3C	cis	cerebellum	SCAN
rs321969	WBSCR16	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78301800-78321600	Weak transcription	Fetal Brain Female	brain
2	chr7:78312400-78313800	Enhancers	Brain Substantia Nigra	brain
3	chr7:78312600-78313800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:78312600-78313800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:78312800-78313800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr7:78313000-78313800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:78313000-78313800	Enhancers	Brain Cingulate Gyrus	brain
8	chr7:78313000-78313800	Enhancers	Brain Hippocampus Middle	brain
9	chr7:78313000-78314800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:78313200-78319600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:78313600-78313800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:78313600-78314000	Enhancers	HUES48 Cell Line	embryonic stem cell

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

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