Variant report

Variant	rs6728372
Chromosome Location	chr2:56899555-56899556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1008079	0.81[EUR][1000 genomes]
rs10164491	0.84[ASN][1000 genomes]
rs1016542	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs10169833	0.81[EUR][1000 genomes]
rs10187925	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10190939	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10193496	0.81[EUR][1000 genomes]
rs11125650	0.82[EUR][1000 genomes]
rs11678164	0.81[EUR][1000 genomes]
rs11889516	0.83[EUR][1000 genomes]
rs12611839	0.88[EUR][1000 genomes]
rs13389774	0.87[EUR][1000 genomes]
rs13392863	0.87[EUR][1000 genomes]
rs13403703	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13427440	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17048326	0.87[EUR][1000 genomes]
rs17048328	0.88[EUR][1000 genomes]
rs1996705	0.81[EUR][1000 genomes]
rs2042118	0.88[EUR][1000 genomes]
rs2042119	0.87[EUR][1000 genomes]
rs2042120	0.85[EUR][1000 genomes]
rs2058993	0.82[EUR][1000 genomes]
rs2072584	0.84[EUR][1000 genomes]
rs2161032	0.81[EUR][1000 genomes]
rs2216494	0.82[EUR][1000 genomes]
rs2870077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948576	0.85[ASN][1000 genomes]
rs4140686	0.83[EUR][1000 genomes]
rs4544483	0.81[EUR][1000 genomes]
rs4566401	0.84[EUR][1000 genomes]
rs4671296	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57457595	0.85[ASN][1000 genomes]
rs59647856	0.87[EUR][1000 genomes]
rs60966744	0.87[EUR][1000 genomes]
rs62161431	0.85[ASN][1000 genomes]
rs62161434	0.84[ASN][1000 genomes]
rs62162355	0.85[EUR][1000 genomes]
rs6545582	0.86[ASN][1000 genomes]
rs6719274	0.82[EUR][1000 genomes]
rs6730195	0.82[EUR][1000 genomes]
rs6732705	0.91[EUR][1000 genomes]
rs6735845	0.81[EUR][1000 genomes]
rs6742821	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556866	0.87[EUR][1000 genomes]
rs7557250	0.89[EUR][1000 genomes]
rs7577567	0.81[EUR][1000 genomes]
rs7587789	0.81[EUR][1000 genomes]
rs918331	0.83[EUR][1000 genomes]
rs965946	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv582051	chr2:56706758-56902709	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1012596	chr2:56761303-56916336	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv535725	chr2:56761303-56916336	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1008859	chr2:56767452-57126026	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535726	chr2:56767452-57126026	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv874179	chr2:56817927-56957466	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874180	chr2:56822558-56957466	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv582058	chr2:56892585-57016392	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv582059	chr2:56892585-57175087	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv535727	chr2:56895497-57059359	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6728372	EFEMP1	cis	cerebellum	SCAN
rs6728372	ACYP2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56898800-56900200	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr2:56899400-56899800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
3	chr2:56899400-56900000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:56899400-56900000	ZNF genes & repeats	Gastric	stomach
5	chr2:56899400-56900600	ZNF genes & repeats	Pancreas	Pancrea

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