Variant report

Variant	rs59469255
Chromosome Location	chr1:59094679-59094680
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59085880..59088538-chr1:59092105..59094981,3	MCF-7	breast:
2	chr1:59041155..59044149-chr1:59093700..59095939,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184292	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10157697	0.86[EUR][1000 genomes]
rs10465804	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11207300	0.81[ASN][1000 genomes]
rs11576450	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578449	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578726	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579130	0.84[EUR][1000 genomes]
rs11579447	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580213	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581243	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582157	0.81[ASN][1000 genomes]
rs11582185	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11584050	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584589	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11587264	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11590060	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11811483	0.87[EUR][1000 genomes]
rs11811899	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562546	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564701	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565004	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12566630	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12567616	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13374003	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13375494	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13375496	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1492719	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15307	0.86[ASN][1000 genomes]
rs170828	0.81[ASN][1000 genomes]
rs17264915	0.81[ASN][1000 genomes]
rs17372453	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2273045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232778	0.86[ASN][1000 genomes]
rs232779	0.86[ASN][1000 genomes]
rs232783	0.86[ASN][1000 genomes]
rs232788	0.86[ASN][1000 genomes]
rs232790	0.86[ASN][1000 genomes]
rs232857	0.86[ASN][1000 genomes]
rs232862	0.86[ASN][1000 genomes]
rs232863	0.86[ASN][1000 genomes]
rs232867	0.86[ASN][1000 genomes]
rs232877	0.86[ASN][1000 genomes]
rs232880	0.86[ASN][1000 genomes]
rs232886	0.86[ASN][1000 genomes]
rs232901	0.86[ASN][1000 genomes]
rs232902	0.86[ASN][1000 genomes]
rs232904	0.86[ASN][1000 genomes]
rs232905	0.86[ASN][1000 genomes]
rs232906	0.89[ASN][1000 genomes]
rs232907	0.89[ASN][1000 genomes]
rs232908	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs232910	0.91[ASN][1000 genomes]
rs232911	0.91[ASN][1000 genomes]
rs2407019	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2746077	0.86[ASN][1000 genomes]
rs2746083	0.81[ASN][1000 genomes]
rs34204484	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35584156	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36084158	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912369	0.86[ASN][1000 genomes]
rs4912372	0.89[ASN][1000 genomes]
rs513436	0.86[ASN][1000 genomes]
rs542750	0.86[ASN][1000 genomes]
rs55742964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56011712	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56097207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57043686	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57166198	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57925801	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58488453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58575274	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58626572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59450768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59590779	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60217618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382465	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60698357	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60869327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61070091	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61203902	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61552468	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661394	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661513	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661808	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6661896	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661922	0.86[ASN][1000 genomes]
rs6661969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675871	0.86[ASN][1000 genomes]
rs688225	0.86[ASN][1000 genomes]
rs72674199	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72676705	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72676710	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72676712	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72676714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676723	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59085800-59094800	Weak transcription	HMEC	breast
2	chr1:59086000-59100600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:59086400-59104000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:59087200-59101600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:59091400-59096400	Weak transcription	Gastric	stomach
6	chr1:59091600-59100400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:59093200-59115400	Weak transcription	NHEK	skin
8	chr1:59094000-59094800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:59094000-59095600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:59094200-59094800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:59094200-59095200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:59094200-59095200	Enhancers	HSMM	muscle
13	chr1:59094200-59095200	Enhancers	HSMMtube	muscle
14	chr1:59094200-59095400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:59094200-59095600	Enhancers	Osteobl	bone
16	chr1:59094400-59095000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:59094400-59095000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:59094600-59095000	Enhancers	Hela-S3	cervix

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