Variant report

Variant	rs2746439
Chromosome Location	chr6:37558561-37558562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1621500	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1738442	0.81[AMR][1000 genomes]
rs1738443	0.81[AMR][1000 genomes]
rs1738444	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1776441	0.85[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2776900	0.90[ASN][1000 genomes]
rs9470635	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2746439	TCP11	cis	parietal	SCAN
rs2746439	GLP1R	cis	parietal	SCAN
rs2746439	MDGA1	cis	parietal	SCAN
rs2746439	ANKS1A	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37552600-37558600	Enhancers	Fetal Brain Male	brain
2	chr6:37553400-37559400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:37556600-37561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:37556600-37562000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:37556600-37567600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:37556800-37559200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:37558400-37558600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:37558400-37560400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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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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