Variant report

Variant	rs3778558
Chromosome Location	chr6:2144252-2144253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11968026	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13437488	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163068	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs163069	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs163070	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs163071	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs163072	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs170930	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17134693	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs180189	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184621	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs186828	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1883871	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883872	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234917	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs234918	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs234919	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs234924	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234925	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234926	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234927	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234928	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234929	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs234930	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs234931	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs234938	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs234939	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs234940	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs234941	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234942	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234943	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234945	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234947	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234948	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs234949	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs234950	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs372304	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3778559	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3800158	1.00[ASN][1000 genomes]
rs3800163	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3800164	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3800165	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800167	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3800168	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3800169	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800170	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs398992	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4140449	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs431112	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs452490	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4959166	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4959167	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959635	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959639	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959641	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4959642	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959643	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959644	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56231942	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59665671	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911073	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934917	1.00[ASN][1000 genomes]
rs72830156	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7740222	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328084	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392369	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9503106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503109	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv522608	chr6:2032259-2203888	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv883387	chr6:2086679-2176239	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
11	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
12	nsv519587	chr6:2097654-2145447	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv524730	chr6:2122454-2145136	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv527808	chr6:2122454-2145447	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2128000-2160800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:2134400-2144400	Weak transcription	Esophagus	oesophagus
3	chr6:2134400-2157400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:2134800-2144400	Weak transcription	Gastric	stomach
5	chr6:2137600-2146600	Weak transcription	Fetal Intestine Small	intestine
6	chr6:2142200-2147600	Weak transcription	Osteobl	bone
7	chr6:2142200-2151600	Weak transcription	HMEC	breast
8	chr6:2142400-2145000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:2142600-2161000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:2142800-2144800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:2142800-2145000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:2143000-2144400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:2143000-2145200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:2143200-2144400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:2143400-2144400	Weak transcription	Lung	lung
16	chr6:2143600-2144400	Weak transcription	Stomach Mucosa	stomach
17	chr6:2143600-2161600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:2143600-2161600	Weak transcription	HepG2	liver
19	chr6:2143800-2144800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr6:2143800-2144800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr6:2144000-2147400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:2144200-2145000	Enhancers	Small Intestine	intestine

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