Variant report

Variant	rs7716600
Chromosome Location	chr5:44875005-44875006
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10059086	0.81[ASN][1000 genomes]
rs10070037	0.81[ASN][1000 genomes]
rs11951760	0.81[ASN][1000 genomes]
rs4329028	0.80[ASN][1000 genomes]
rs4866783	0.81[ASN][1000 genomes]
rs727304	1.00[JPT][hapmap]
rs9292913	0.80[ASN][1000 genomes]
rs9292914	0.81[ASN][1000 genomes]
rs9292915	0.80[ASN][1000 genomes]
rs930395	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[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	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv881564	chr5:44783255-44914579	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv880397	chr5:44800665-44939293	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv880483	chr5:44827292-45038026	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Breast cancer	20872241	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7716600	LOC100132356	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44869600-44875200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:44872600-44875800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:44874800-44875800	Enhancers	Hela-S3	cervix
4	chr5:44874800-44876000	Enhancers	HMEC	breast
5	chr5:44875000-44875200	Enhancers	GM12878-XiMat	blood
6	chr5:44875000-44875800	Enhancers	NHEK	skin
7	chr5:44875000-44876000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr5:44875000-44876400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr5:44875000-44876400	Enhancers	HUVEC	blood vessel
10	chr5:44875000-44877000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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