Variant report

Variant	rs2363557
Chromosome Location	chr1:215320460-215320461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:215125696..215126808-chr1:215319275..215320710,4	MCF-7	breast:

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10127521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10127656	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10746454	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10746455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779639	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10779640	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10779642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779644	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10779645	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs10779646	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10779647	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10779649	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779650	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10779651	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[YRI][hapmap];0.97[ASN][1000 genomes]
rs10779652	0.89[ASN][1000 genomes]
rs10864150	0.95[CEU][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes]
rs10864152	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10864154	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10864157	0.86[ASN][1000 genomes]
rs11120495	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120496	0.82[ASN][1000 genomes]
rs11120497	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120498	0.82[ASN][1000 genomes]
rs11120499	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11120500	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120506	0.84[ASN][1000 genomes]
rs11120508	0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11120511	0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11120513	0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11120516	0.83[ASN][1000 genomes]
rs11120519	0.82[CHD][hapmap]
rs1112101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12031308	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs12039875	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs12061916	0.82[ASN][1000 genomes]
rs12062098	0.91[ASN][1000 genomes]
rs12068734	0.84[ASN][1000 genomes]
rs12120091	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12121761	0.90[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12135076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138497	0.97[ASN][1000 genomes]
rs12141874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12143339	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12410041	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12411068	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12567520	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12740245	0.84[CHB][hapmap]
rs12742137	0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12753507	0.84[CHB][hapmap]
rs1339405	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1339406	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1361340	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1416647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1556906	0.83[YRI][hapmap]
rs1578137	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2027320	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2363554	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2363556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2363558	0.91[AMR][1000 genomes]
rs2363559	0.91[AMR][1000 genomes]
rs2363560	0.90[AMR][1000 genomes]
rs2363564	0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs2363565	0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2363566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2363567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2885812	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs2885813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2885815	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3931584	0.83[ASN][1000 genomes]
rs3931585	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4262516	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4269745	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4271184	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs4300189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4303048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375232	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4411107	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4428856	0.82[ASN][1000 genomes]
rs4497183	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4509552	0.84[ASN][1000 genomes]
rs4509553	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4531266	0.94[CEU][hapmap];0.94[CHB][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4548407	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4556330	0.86[CHB][hapmap]
rs4571941	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4573492	0.82[ASN][1000 genomes]
rs4607848	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4655276	0.84[ASN][1000 genomes]
rs4655277	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[ASN][1000 genomes]
rs4655278	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4655391	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4655392	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4655393	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4655394	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4655395	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818297	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61818299	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61818320	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818328	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6662353	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6666828	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6667764	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6672978	0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6673739	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6675926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678758	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683041	0.82[ASN][1000 genomes]
rs6684084	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[ASN][1000 genomes]
rs6688713	0.95[CEU][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes]
rs6695343	0.89[ASN][1000 genomes]
rs6695967	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6699161	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs72735359	1.00[ASN][1000 genomes]
rs7410928	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7417100	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs7513709	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7516689	0.95[CEU][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes]
rs7540029	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541543	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7547572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7547655	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7549136	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs7551415	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7555013	0.84[AMR][1000 genomes]
rs7555727	0.83[AMR][1000 genomes]
rs9793382	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9793690	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][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	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2363557	FDX1	trans	cerebellum	SCAN
rs2363557	SYT14	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215314000-215333800	Weak transcription	NHDF-Ad	bronchial
2	chr1:215318400-215320600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:215320000-215322400	Weak transcription	NHLF	lung
4	chr1:215320000-215333600	Weak transcription	Osteobl	bone
5	chr1:215320000-215333800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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