Variant report

Variant	rs6960580
Chromosome Location	chr7:39336413-39336414
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11973905	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11981474	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12701709	0.81[CHB][hapmap]
rs12701728	0.82[JPT][hapmap]
rs3923295	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4318977	0.82[CHB][hapmap]
rs4358689	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4377848	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4629764	0.82[CHB][hapmap]
rs6951074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964993	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6968121	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73118070	1.00[ASN][1000 genomes]
rs73121820	1.00[ASN][1000 genomes]
rs73128427	0.83[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	nsv1015572	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv538821	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv887969	chr7:39265429-39391875	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6960580	ANLN	cis	cerebellum	SCAN
rs6960580	TUBA8	trans	cerebellum	SCAN
rs6960580	RALA	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39330200-39337200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:39332000-39339400	Weak transcription	Aorta	Aorta
3	chr7:39333600-39337400	Enhancers	Duodenum Mucosa	Duodenum
4	chr7:39334200-39336600	Enhancers	Fetal Intestine Large	intestine
5	chr7:39334200-39337200	Enhancers	Fetal Intestine Small	intestine
6	chr7:39335600-39339400	Weak transcription	Right Atrium	heart
7	chr7:39336200-39339400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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