Variant report

Variant	rs1842962
Chromosome Location	chr8:85516746-85516747
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:84312343..84312899-chr8:85516697..85517398,2	MCF-7	breast:
2	chr8:83628706..83629529-chr8:85516684..85517325,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1006976	0.80[GIH][hapmap]
rs10093758	0.85[EUR][1000 genomes]
rs10094897	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10096903	0.85[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs10104232	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10109730	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10112163	0.84[CEU][hapmap]
rs10504807	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap]
rs10504808	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10958225	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10958227	0.80[GIH][hapmap]
rs11985369	0.86[CEU][hapmap]
rs11989750	0.85[CEU][hapmap]
rs1252199	0.91[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs1252200	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252202	0.85[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252204	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1252205	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1252208	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1252209	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252211	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252212	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1252213	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1252215	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1252216	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs1252217	0.86[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap]
rs1252219	1.00[JPT][hapmap]
rs1252220	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252221	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252222	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252223	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1252224	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1252225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1268561	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1268562	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1351724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1466522	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1483353	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1483354	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1488706	0.86[CEU][hapmap]
rs1488709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs1565225	0.85[GIH][hapmap];0.80[MEX][hapmap]
rs1626630	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1681355	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16912908	0.81[JPT][hapmap]
rs16913056	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16913090	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1730816	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1730824	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1730826	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1730827	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17726976	0.85[CEU][hapmap]
rs17794266	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17794302	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17794614	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2220426	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2634044	0.80[GIH][hapmap]
rs2634047	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs2634051	0.80[GIH][hapmap]
rs2718968	0.84[CEU][hapmap]
rs2718972	0.81[TSI][hapmap]
rs2718973	0.80[GIH][hapmap]
rs2718975	0.89[CEU][hapmap]
rs2718976	0.81[CEU][hapmap]
rs28405987	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28446816	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28676726	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28695582	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28760488	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2930064	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930065	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs2957790	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2970009	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs3101802	0.81[JPT][hapmap]
rs3109781	0.94[ASN][1000 genomes]
rs4302839	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4416819	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs56165928	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56335539	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66683633	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6986632	0.86[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs6988126	0.81[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs6996709	0.80[GIH][hapmap]
rs6997041	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7010348	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7014897	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72681013	0.90[ASN][1000 genomes]
rs729076	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs7815917	0.86[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs7819269	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7820496	0.80[EUR][1000 genomes]
rs7828076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7831433	0.86[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs7840920	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7840925	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7841984	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap]
rs7842614	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs957816	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs9886561	0.83[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9886620	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs9987099	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1842962	RALYL	cis	cerebellum	SCAN
rs1842962	WWP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:85514800-85516800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr8:85514800-85517000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr8:85514800-85517000	Enhancers	Liver	Liver
4	chr8:85515000-85516800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:85515000-85518000	Weak transcription	Fetal Kidney	kidney
6	chr8:85515800-85517000	Enhancers	Fetal Intestine Large	intestine
7	chr8:85515800-85517000	Enhancers	Fetal Intestine Small	intestine
8	chr8:85515800-85517200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr8:85516200-85516800	Enhancers	Brain Germinal Matrix	brain
10	chr8:85516200-85517000	Enhancers	Fetal Brain Male	brain
11	chr8:85516400-85516800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:85516400-85516800	Enhancers	Fetal Lung	lung
13	chr8:85516400-85517200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr8:85516600-85516800	Flanking Active TSS	Fetal Brain Female	brain
15	chr8:85516600-85517000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr8:85516600-85517000	Active TSS	Brain Anterior Caudate	brain
17	chr8:85516600-85517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr8:85516600-85523000	Weak transcription	Brain Angular Gyrus	brain

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