Variant report

Variant	rs6460672
Chromosome Location	chr7:71021037-71021038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13238757	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34860529	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35601662	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4128374	0.83[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs4272248	0.92[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4719138	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4719147	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs6460662	0.91[CEU][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6460666	0.86[CHD][hapmap]
rs6460667	0.86[AFR][1000 genomes]
rs6460669	0.83[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs6947549	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6969457	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6973852	0.88[CHD][hapmap]
rs7790450	0.80[ASN][1000 genomes]
rs7793440	0.81[ASN][1000 genomes]
rs7808739	0.83[ASN][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	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1033783	chr7:70955277-71023877	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6460672	CLDN4	cis	cerebellum	SCAN
rs6460672	CLDN3	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70988000-71023800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:71004000-71023600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:71007200-71023400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:71013600-71023400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:71016600-71024200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:71016800-71023200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:71017400-71024400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:71019800-71024200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:71020800-71024000	Weak transcription	Fetal Brain Male	brain

Quick Search:

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

what's new

Quick links