Variant report

Variant	rs1304179
Chromosome Location	chr20:15296031-15296032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12480304	0.87[YRI][hapmap]
rs16995525	1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs17299383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6034142	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6034145	1.00[JPT][hapmap]
rs6034151	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6034152	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6034155	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6043164	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6043165	1.00[JPT][hapmap]
rs6043166	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6043199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[ASN][1000 genomes]
rs6043201	0.87[ASN][1000 genomes]
rs6043225	0.86[GIH][hapmap]
rs6079727	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6079728	1.00[JPT][hapmap]
rs6079753	1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs8115953	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065152	chr20:14781684-15305258	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1062252	chr20:14964258-15547739	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv544206	chr20:14964258-15547739	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv524481	chr20:15007730-15382919	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv916795	chr20:15041479-15345528	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1060275	chr20:15084485-15327541	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1058890	chr20:15234769-15388360	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2755557	chr20:15250014-15323282	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv912787	chr20:15275538-15309089	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv912788	chr20:15275538-15332749	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv912789	chr20:15275538-15352001	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv2757712	chr20:15282448-15331007	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv2758786	chr20:15282448-15331007	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv585583	chr20:15289701-15303701	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv1830261	chr20:15291552-15304048	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv585584	chr20:15292533-15303701	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1304179	MGC44328	cis	cerebellum	SCAN
rs1304179	FLRT3	cis	cerebellum	SCAN
rs1304179	OVOL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15291600-15297000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr20:15295400-15297200	Enhancers	GM12878-XiMat	blood
3	chr20:15296000-15296200	Enhancers	Primary monocytes fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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