Variant report

Variant	rs6828559
Chromosome Location	chr4:54235363-54235364
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54233149..54235683-chr4:54236271..54238377,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10000746	0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs10001201	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10005424	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10007903	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10011259	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs10011394	0.80[ASN][1000 genomes]
rs10017903	0.82[EUR][1000 genomes]
rs10021541	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10028142	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10032903	0.80[ASN][1000 genomes]
rs1021099	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11133266	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs11133276	0.85[CEU][hapmap]
rs11722866	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11723755	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11725230	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11731499	0.82[EUR][1000 genomes]
rs11734039	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11734681	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11944047	0.81[GIH][hapmap]
rs11947256	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12507563	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12507739	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs12508701	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12511088	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12511253	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12642403	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs12649718	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651390	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13150384	0.80[ASN][1000 genomes]
rs1471597	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1481819	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1481824	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1531748	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1600795	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs17082893	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.80[ASN][1000 genomes]
rs17520800	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2090117	0.81[CEU][hapmap]
rs2271554	0.82[EUR][1000 genomes]
rs2271559	0.90[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2412447	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412488	0.81[CEU][hapmap]
rs28414913	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28459503	0.84[ASN][1000 genomes]
rs35089837	0.80[ASN][1000 genomes]
rs35499169	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36011216	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3765158	0.81[CEU][hapmap]
rs3811782	0.83[EUR][1000 genomes]
rs3811785	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4864759	0.82[EUR][1000 genomes]
rs4864760	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864767	0.91[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs56998298	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554098	0.86[LWK][hapmap]
rs6554100	0.83[EUR][1000 genomes]
rs6554104	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554105	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554106	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6554109	0.81[GIH][hapmap]
rs6818788	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6821328	0.81[LWK][hapmap]
rs6822201	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap]
rs6825364	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6833766	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6834934	0.83[EUR][1000 genomes]
rs6835629	0.81[GIH][hapmap]
rs6838260	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6839922	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6840343	0.82[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs6840530	0.91[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs6848887	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852884	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs6857024	0.83[EUR][1000 genomes]
rs6857869	0.80[EUR][1000 genomes]
rs7655975	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682199	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7686177	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7686876	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688853	0.80[ASN][1000 genomes]
rs7689981	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7690908	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7691578	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7697622	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7698792	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs931181	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931182	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs9312639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs980987	0.81[EUR][1000 genomes]
rs9995284	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9996883	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6828559	TYW1B	trans	parietal	SCAN
rs6828559	ZNF585A	cis	Frontal Cortex	GTEx
rs6828559	EXOC1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54233000-54238600	Weak transcription	Aorta	Aorta
2	chr4:54233000-54243200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr4:54233200-54235400	Weak transcription	K562	blood
4	chr4:54234600-54235400	Enhancers	Thymus	Thymus

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