Variant report

Variant	rs12498799
Chromosome Location	chr4:20657352-20657353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10516361	0.88[ASN][1000 genomes]
rs1080125	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805218	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11721944	0.88[ASN][1000 genomes]
rs11733451	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735866	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736309	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736477	0.88[ASN][1000 genomes]
rs11737893	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503714	0.88[ASN][1000 genomes]
rs12510666	0.94[ASN][1000 genomes]
rs1365580	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1365581	0.92[ASN][1000 genomes]
rs1426882	0.86[ASN][1000 genomes]
rs16869823	0.98[ASN][1000 genomes]
rs16869859	0.88[ASN][1000 genomes]
rs16869884	0.88[ASN][1000 genomes]
rs17552950	0.88[ASN][1000 genomes]
rs17622121	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28439580	0.88[ASN][1000 genomes]
rs2874831	0.88[ASN][1000 genomes]
rs56267013	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57364495	0.88[ASN][1000 genomes]
rs59687189	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61790721	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61790747	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62410066	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62410087	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62410132	0.88[ASN][1000 genomes]
rs62410133	0.88[ASN][1000 genomes]
rs62410158	0.81[ASN][1000 genomes]
rs62411661	0.81[ASN][1000 genomes]
rs6831523	0.81[ASN][1000 genomes]
rs73101456	0.96[ASN][1000 genomes]
rs964020	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829875	chr4:20502895-20680956	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	89 gene(s)	inside rSNPs	diseases
2	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12498799	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20654400-20659600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:20654600-20673800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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