Variant report

Variant	rs302588
Chromosome Location	chr6:39678419-39678420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11752840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs11754307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs11754807	0.82[MEX][hapmap]
rs11755914	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1380343	0.95[YRI][hapmap]
rs149242	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs149607	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1563770	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs159956	0.84[AFR][1000 genomes]
rs159957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs159958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs160019	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs160020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs160021	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs160023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs160024	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs160028	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs160030	0.85[AFR][1000 genomes]
rs160032	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2199174	0.96[EUR][1000 genomes]
rs2446644	0.89[YRI][hapmap]
rs2446646	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs2446649	1.00[CHB][hapmap]
rs2465672	1.00[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2466410	0.83[AFR][1000 genomes]
rs2499450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs2499452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs302547	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs302548	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs302561	0.84[AFR][1000 genomes]
rs302563	0.91[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs302564	0.92[AFR][1000 genomes]
rs302565	0.85[AFR][1000 genomes]
rs302567	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs302568	0.85[AFR][1000 genomes]
rs302570	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs302572	0.91[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs302573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs302574	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs302575	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs302579	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs302586	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs302587	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs302589	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs302591	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs302592	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs302593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs302594	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs302595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs302596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs303649	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs303653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs303661	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs303675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303677	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs303700	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs307437	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55815613	0.99[EUR][1000 genomes]
rs55941685	0.96[EUR][1000 genomes]
rs56130116	0.96[EUR][1000 genomes]
rs62402464	0.99[EUR][1000 genomes]
rs62402465	0.96[EUR][1000 genomes]
rs62402466	0.96[EUR][1000 genomes]
rs62403326	0.96[EUR][1000 genomes]
rs62403334	0.96[EUR][1000 genomes]
rs62403359	0.99[EUR][1000 genomes]
rs62405160	0.99[EUR][1000 genomes]
rs964116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs302588	POLR1C	cis	parietal	SCAN
rs302588	GUCA1A	cis	cerebellum	SCAN
rs302588	TDRG1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39665200-39680000	Weak transcription	Pancreas	Pancrea
2	chr6:39676200-39680800	Weak transcription	Brain Substantia Nigra	brain
3	chr6:39676200-39692600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:39676600-39681000	Weak transcription	NHDF-Ad	bronchial
5	chr6:39676800-39678800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr6:39677000-39678600	Enhancers	Brain Hippocampus Middle	brain
7	chr6:39677200-39678600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr6:39678200-39680800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:39678200-39681400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:39678200-39681600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:39678200-39692400	Weak transcription	H9 Cell Line	embryonic stem cell

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