Variant report

Variant	rs6728723
Chromosome Location	chr2:99716883-99716884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10865030	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs11123769	0.87[EUR][1000 genomes]
rs12993310	0.86[EUR][1000 genomes]
rs13404012	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13427090	0.85[ASN][1000 genomes]
rs1487271	0.86[EUR][1000 genomes]
rs1565054	0.84[EUR][1000 genomes]
rs1843807	0.86[EUR][1000 genomes]
rs1922625	0.80[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs2091798	0.84[EUR][1000 genomes]
rs4522654	0.80[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs4850896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851189	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851191	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4851194	0.86[EUR][1000 genomes]
rs4851199	0.80[CEU][hapmap]
rs6542871	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6749029	0.80[CEU][hapmap]
rs7579999	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7586635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7602401	0.86[EUR][1000 genomes]
rs7603388	0.80[CEU][hapmap]
rs7606279	0.80[CEU][hapmap]
rs896884	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6728723	LYG1	cis	parietal	SCAN
rs6728723	ARID5A	cis	parietal	SCAN
rs6728723	MRPL30	Cis_1M	lymphoblastoid	RTeQTL
rs6728723	LIPT1	cis	parietal	SCAN
rs6728723	TSGA10	cis	cerebellum	SCAN
rs6728723	LIPT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99703400-99717800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99712600-99718000	Weak transcription	Adipose Nuclei	Adipose

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