Variant report

Variant	rs239853
Chromosome Location	chr6:54759014-54759015
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	chr6:54758702..54760512-chr6:54764567..54767361,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1028423	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056630	0.85[ASN][1000 genomes]
rs1503137	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs1503150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16886072	1.00[CHB][hapmap]
rs16886073	1.00[CHB][hapmap]
rs16886088	1.00[CHB][hapmap]
rs16886105	1.00[CHB][hapmap]
rs171226	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1738459	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs183011	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1910352	1.00[CHB][hapmap]
rs2397176	0.92[ASN][1000 genomes]
rs239780	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239791	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239797	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239799	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs239807	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239808	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239810	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239827	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239828	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[ASN][1000 genomes]
rs239829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239832	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239835	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239843	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239844	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239845	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239846	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239847	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239849	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239851	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35620314	0.84[ASN][1000 genomes]
rs378853	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs398483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs406149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41431945	1.00[CHB][hapmap]
rs57835829	0.85[ASN][1000 genomes]
rs6917766	0.85[ASN][1000 genomes]
rs73431470	0.92[ASN][1000 genomes]
rs7453441	1.00[CHB][hapmap]
rs7739951	1.00[CHB][hapmap]
rs7743188	1.00[CHB][hapmap]
rs7749972	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773204	1.00[CHB][hapmap]
rs9349735	1.00[CHB][hapmap]
rs9367588	1.00[CHB][hapmap]
rs9367589	1.00[CHB][hapmap]
rs9367596	1.00[CHB][hapmap]
rs9370335	1.00[CHB][hapmap]
rs9382377	1.00[CHB][hapmap]
rs9382388	1.00[CHB][hapmap]
rs9395992	1.00[CHB][hapmap]
rs9475077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs239853	GSTA2	cis	parietal	SCAN
rs239853	NHSL2	trans	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
2	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:54757200-54763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:54757800-54760600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54757800-54763200	Weak transcription	NHEK	skin
6	chr6:54758000-54761200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54758000-54769400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:54758000-54775000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:54758400-54761000	Weak transcription	HMEC	breast
10	chr6:54758600-54759600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr6:54758800-54759200	Enhancers	Fetal Intestine Large	intestine
12	chr6:54758800-54759200	Enhancers	Fetal Intestine Small	intestine
13	chr6:54759000-54759200	Enhancers	Rectal Mucosa Donor 29	rectum

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