Variant report

Variant	rs539958
Chromosome Location	chr6:160772842-160772843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10945670	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1317652	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1605963	0.85[EUR][1000 genomes]
rs1605964	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1605965	0.90[ASN][1000 genomes]
rs2136676	0.85[EUR][1000 genomes]
rs2313453	0.85[EUR][1000 genomes]
rs2661845	0.83[ASN][1000 genomes]
rs2665357	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2872317	0.85[EUR][1000 genomes]
rs3105748	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs3105749	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs3105752	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs3123633	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs3123634	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs3127574	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs316172	0.87[ASN][1000 genomes]
rs316177	0.86[ASN][1000 genomes]
rs366608	0.87[ASN][1000 genomes]
rs367213	0.87[ASN][1000 genomes]
rs372665	0.87[ASN][1000 genomes]
rs376563	0.82[CEU][hapmap]
rs377551	0.95[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.94[ASN][1000 genomes]
rs383420	0.87[ASN][1000 genomes]
rs394468	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs394487	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.94[ASN][1000 genomes]
rs396843	0.87[ASN][1000 genomes]
rs401746	0.86[ASN][1000 genomes]
rs405405	0.94[ASN][1000 genomes]
rs416879	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235926	0.86[EUR][1000 genomes]
rs423961	0.87[ASN][1000 genomes]
rs425983	0.87[ASN][1000 genomes]
rs431747	0.87[ASN][1000 genomes]
rs435421	0.87[ASN][1000 genomes]
rs445849	0.87[ASN][1000 genomes]
rs4709425	0.86[EUR][1000 genomes]
rs4709426	0.85[EUR][1000 genomes]
rs474513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs486339	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486359	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs487152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs490275	0.87[ASN][1000 genomes]
rs501470	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs505870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs509707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512077	0.85[YRI][hapmap]
rs518295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs519118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs520685	0.88[ASN][1000 genomes]
rs520829	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs537937	0.87[ASN][1000 genomes]
rs539298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541091	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs543159	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547290	0.87[ASN][1000 genomes]
rs555754	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs569919	0.84[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs575719	0.82[ASN][1000 genomes]
rs575796	0.84[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs581556	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622217	0.92[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs624319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634916	0.87[ASN][1000 genomes]
rs637614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641990	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs668871	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs673259	0.93[ASN][1000 genomes]
rs673736	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs675162	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6905958	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6923921	0.86[EUR][1000 genomes]
rs695174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884742	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs9346816	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9364552	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1030746	chr6:160592321-160867031	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538493	chr6:160592321-160867031	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030171	chr6:160648469-161091864	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv886809	chr6:160670494-160979275	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv886810	chr6:160700769-160897872	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv886811	chr6:160700769-161070990	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv886812	chr6:160706661-161024848	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160770400-160775800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:160770800-160776200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:160771200-160775800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:160771200-160780400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:160771400-160775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:160771400-160775800	Weak transcription	Esophagus	oesophagus
7	chr6:160771600-160775800	Weak transcription	NHEK	skin
8	chr6:160771600-160776000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:160771600-160776000	Weak transcription	Adipose Nuclei	Adipose
10	chr6:160771800-160775600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:160772000-160773000	Weak transcription	Ovary	ovary
12	chr6:160772000-160773000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr6:160772000-160773400	Enhancers	Liver	Liver
14	chr6:160772000-160776000	Weak transcription	Placenta	Placenta
15	chr6:160772000-160777400	Weak transcription	Gastric	stomach
16	chr6:160772000-160778000	Weak transcription	Psoas Muscle	Psoas
17	chr6:160772000-160778000	Enhancers	HepG2	liver
18	chr6:160772800-160773200	Flanking Active TSS	A549	lung
19	chr6:160772800-160773400	Flanking Active TSS	Aorta	Aorta
20	chr6:160772800-160773400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:160772800-160775800	Weak transcription	Stomach Mucosa	stomach

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