Variant report

Variant	rs3121212
Chromosome Location	chr13:51218559-51218560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12853944	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1935174	0.92[ASN][1000 genomes]
rs2794460	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2796843	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3095526	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3116599	1.00[ASW][hapmap]
rs3116618	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3116619	0.91[ASN][1000 genomes]
rs3116620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121210	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3121211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3123270	0.92[ASN][1000 genomes]
rs628413	0.82[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs637310	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs640923	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs706597	0.84[ASN][1000 genomes]
rs797474	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	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription 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	1256 gene(s)	inside rSNPs	diseases
2	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3121212	GUCY1B2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51210800-51223800	Weak transcription	Fetal Thymus	thymus
2	chr13:51218200-51218800	Enhancers	HepG2	liver
3	chr13:51218200-51220000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:51218200-51220400	Enhancers	HMEC	breast
5	chr13:51218400-51219200	Enhancers	HSMMtube	muscle
6	chr13:51218400-51220400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:51218400-51220600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:51218400-51220600	Enhancers	NHEK	skin

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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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