Variant report

Variant	rs2595249
Chromosome Location	chr3:159019946-159019947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1020470	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1077544	0.95[CHB][hapmap]
rs11921372	0.82[CEU][hapmap]
rs13314849	0.87[ASN][1000 genomes]
rs1449007	0.98[ASN][1000 genomes]
rs1449008	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1449009	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1449022	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1449026	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1449028	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs1900860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs1967363	0.82[CEU][hapmap]
rs2004299	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap]
rs2044704	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2122145	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2244434	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2595233	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs2595235	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2595237	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2595240	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2595241	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2595251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2595261	0.95[CHB][hapmap]
rs2621281	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2621283	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2621285	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2621286	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2621293	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2621296	0.95[ASN][1000 genomes]
rs2621303	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2621304	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2621305	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2621307	0.96[ASN][1000 genomes]
rs2621308	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2621309	0.99[ASN][1000 genomes]
rs2922407	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3903320	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7624604	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs895877	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2595249	RSRC1	cis	parietal	SCAN
rs2595249	YDJC	trans	parietal	SCAN
rs2595249	SCHIP1	cis	parietal	SCAN
rs2595249	IQCJ	cis	parietal	SCAN
rs2595249	LEKR1	cis	parietal	SCAN
rs2595249	RSRC1	cis	cerebellum	SCAN
rs2595249	ACCN2	trans	parietal	SCAN
rs2595249	NMD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159017400-159021800	Weak transcription	Fetal Brain Male	brain

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