Variant report

Variant	rs13398352
Chromosome Location	chr2:187178229-187178230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10169008	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169206	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177153	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190003	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10196955	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10198525	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10200749	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10205170	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208643	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1037241	0.89[ASN][1000 genomes]
rs10497671	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931240	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680486	0.89[ASN][1000 genomes]
rs11688988	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692028	0.89[ASN][1000 genomes]
rs11693797	0.89[ASN][1000 genomes]
rs11888880	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11888881	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898666	0.89[ASN][1000 genomes]
rs12328822	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13393891	0.89[ASN][1000 genomes]
rs13397188	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448855	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448857	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044683	0.89[ASN][1000 genomes]
rs2084489	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34234405	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719959	0.89[ASN][1000 genomes]
rs61226319	0.84[ASN][1000 genomes]
rs6434167	0.89[ASN][1000 genomes]
rs6434174	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710436	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6715493	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716324	0.89[ASN][1000 genomes]
rs6717505	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717525	0.89[ASN][1000 genomes]
rs6721789	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6728400	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731567	0.89[ASN][1000 genomes]
rs72893450	0.89[ASN][1000 genomes]
rs7582412	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585889	0.89[ASN][1000 genomes]
rs7585905	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7588607	0.89[ASN][1000 genomes]
rs7597954	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7606920	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288129	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv817325	chr2:186625679-187200841	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1014726	chr2:187036909-187213113	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv536078	chr2:187036909-187213113	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1006411	chr2:187150025-187291081	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv536079	chr2:187150025-187291081	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13398352	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187171400-187179400	Weak transcription	Brain Substantia Nigra	brain
2	chr2:187173200-187192200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:187173600-187190000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:187177000-187179200	Weak transcription	Ovary	ovary
5	chr2:187177600-187178600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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