Variant report

Variant	rs887719
Chromosome Location	chr7:21184273-21184274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs11531486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17143980	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2390480	1.00[EUR][1000 genomes]
rs35022772	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273757	1.00[EUR][1000 genomes]
rs4534047	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56750732	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58465671	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62439797	0.98[ASN][1000 genomes]
rs62439798	0.93[ASN][1000 genomes]
rs62439800	0.96[ASN][1000 genomes]
rs875928	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs887718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639369	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830920	chr7:21014535-21201580	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	esv3478244	chr7:21044211-21417347	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3478245	chr7:21044211-21417347	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1020852	chr7:21060791-21375050	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv538799	chr7:21060791-21375050	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs887719	DUSP2	trans	brain	seeQTL
rs887719	HS3ST2	trans	brain	seeQTL
rs887719	PDYN	trans	brain	seeQTL
rs887719	LAMB3	trans	brain	seeQTL
rs887719	SERTAD1	trans	brain	seeQTL
rs887719	STK40	trans	brain	seeQTL
rs887719	SLC2A3	trans	brain	seeQTL
rs887719	GPR3	trans	brain	seeQTL
rs887719	ANXA8L2	trans	brain	seeQTL
rs887719	INHBA	trans	brain	seeQTL
rs887719	FCER2	trans	brain	seeQTL
rs887719	WNT1	trans	brain	seeQTL
rs887719	SH3BP1	trans	brain	seeQTL
rs887719	ADAD2	trans	brain	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21183800-21185600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:21184000-21185600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:21184200-21184400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	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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