Variant report

Variant	rs704834
Chromosome Location	chr1:176189141-176189142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176182002..176183788-chr1:176187433..176190030,2	K562	blood:
2	chr1:176175139..176178556-chr1:176187821..176190649,4	K562	blood:

Variant related genes	Relation type
ENSG00000236021	Chromatin interaction
ENSG00000143207	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10458350	0.86[JPT][hapmap]
rs10798445	0.86[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10913152	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913166	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11810706	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs12117377	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12121951	0.83[EUR][1000 genomes]
rs12138008	0.84[CEU][hapmap]
rs12729524	0.86[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs12731148	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12758275	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393763	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs184764	0.86[JPT][hapmap]
rs1858537	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs191606	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2039230	0.86[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2102479	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2175178	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455730	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2455732	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2455749	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2455762	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2455764	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2457418	0.86[CEU][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2481628	0.86[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2481630	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs2481631	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs2481633	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs2481655	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs2481662	0.80[EUR][1000 genomes]
rs2487144	0.86[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2502823	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs2502831	0.86[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2502845	0.86[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap]
rs2504473	0.86[JPT][hapmap]
rs2504493	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2504501	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34612848	0.84[EUR][1000 genomes]
rs352330	0.86[JPT][hapmap]
rs352334	0.86[JPT][hapmap]
rs35907544	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924562	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3962371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4298694	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs482228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs501142	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs513354	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs520661	0.90[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs534088	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs542742	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs596859	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs617078	0.86[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs659279	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6665385	0.86[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs668154	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6687280	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6697860	0.85[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs6700932	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670143	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs679728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs704829	0.86[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs71645275	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549160	0.81[JPT][hapmap]
rs791743	0.86[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs791746	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs791747	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs791750	0.83[EUR][1000 genomes]
rs791751	0.86[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs791752	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs791753	0.85[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs813180	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425447	0.86[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs944365	0.80[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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs704834	VAMP4	cis	parietal	SCAN
rs704834	EME2	trans	cerebellum	SCAN
rs704834	FMO1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176177600-176198600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:176178200-176189400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:176178200-176193800	Weak transcription	Pancreas	Pancrea
4	chr1:176186000-176221400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:176187200-176193600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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