Variant report

Variant	rs11578336
Chromosome Location	chr1:166958710-166958711
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr1:166958159-166958874	H1-hESC	embryonic stem cell:	n/a	chr1:166958496-166958505 chr1:166958469-166958478 chr1:166958337-166958346
2	E2F6	chr1:166958303-166958889	H1-hESC	embryonic stem cell:	n/a	chr1:166958496-166958505 chr1:166958469-166958478 chr1:166958337-166958346
3	POLR2A	chr1:166958580-166958842	MCF-7	breast:	n/a	n/a
4	MYC	chr1:166958661-166958800	MCF-7	breast:	n/a	chr1:166958778-166958788

Variant related genes	Relation type
MAEL	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1041238	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10918600	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs10918603	0.87[CHD][hapmap];1.00[GIH][hapmap]
rs10918607	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs10918608	0.83[ASN][1000 genomes]
rs11579987	0.80[CHD][hapmap];0.95[GIH][hapmap]
rs11802666	0.85[ASN][1000 genomes]
rs11805946	0.86[ASN][1000 genomes]
rs12126991	0.88[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs12131832	0.82[ASN][1000 genomes]
rs12133327	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs12134016	0.88[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap]
rs12564877	0.83[ASN][1000 genomes]
rs12569084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2038022	0.80[CHD][hapmap]
rs2235184	0.80[CHD][hapmap];0.95[GIH][hapmap]
rs2296837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2312487	0.84[ASN][1000 genomes]
rs2312675	0.80[CHB][hapmap]
rs3736988	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs41269702	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61447801	0.86[ASN][1000 genomes]
rs61606407	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427047	0.80[CHD][hapmap];0.95[GIH][hapmap]
rs6427053	0.88[CHB][hapmap];0.97[CHD][hapmap];0.80[JPT][hapmap]
rs6655947	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs6660048	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs6662130	0.86[ASN][1000 genomes]
rs6665341	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669886	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6673622	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6673720	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs6677644	0.87[CHD][hapmap]
rs6681562	0.82[ASN][1000 genomes]
rs6681571	0.82[ASN][1000 genomes]
rs6682062	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695162	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6695609	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs6696203	0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6697417	0.87[ASN][1000 genomes]
rs6699159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs742048	0.95[GIH][hapmap]
rs7511933	0.86[ASN][1000 genomes]
rs7518155	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7520897	0.87[CHD][hapmap]
rs7528849	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7533688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7545806	0.87[CHD][hapmap];1.00[GIH][hapmap]
rs7545911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7550698	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1004148	chr1:166951869-167016311	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2750815	chr1:166953866-167180342	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11578336	RGS4	cis	parietal	SCAN
rs11578336	TBX19	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166958400-166958800	Active TSS	Spleen	Spleen
2	chr1:166958400-166959000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:166958400-166964600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:166958600-166959200	Active TSS	Placenta	Placenta

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