Variant report

Variant	rs279804
Chromosome Location	chr19:21465099-21465100
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	chr19:21462003..21463957-chr19:21465037..21467413,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF738-5	chr19:21465045-21465156	ucscGeneNc_uc002nqb_2

Extended variants
information (count: 87 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1114305	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2086319	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs2434996	0.80[EUR][1000 genomes]
rs2562402	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2562409	0.85[EUR][1000 genomes]
rs2562415	0.85[EUR][1000 genomes]
rs2562435	1.00[CHB][hapmap]
rs2562438	0.92[EUR][1000 genomes]
rs2650797	0.85[EUR][1000 genomes]
rs2650798	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2650842	0.92[EUR][1000 genomes]
rs2650849	0.85[EUR][1000 genomes]
rs2650851	0.85[EUR][1000 genomes]
rs279805	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279810	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279811	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279812	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279814	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279815	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279816	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279817	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs279818	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs279819	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs279820	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2914626	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2914627	0.85[EUR][1000 genomes]
rs2914645	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2928188	0.86[EUR][1000 genomes]
rs2928209	0.92[EUR][1000 genomes]
rs2928216	0.92[EUR][1000 genomes]
rs2928218	0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs2937157	0.85[EUR][1000 genomes]
rs2937174	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2968022	0.92[EUR][1000 genomes]
rs2968023	0.92[EUR][1000 genomes]
rs2968024	0.92[EUR][1000 genomes]
rs2968041	0.85[EUR][1000 genomes]
rs2968045	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2968046	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2968066	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2968082	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2968086	0.92[EUR][1000 genomes]
rs472472	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs475162	0.92[EUR][1000 genomes]
rs476376	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs478046	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487991	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs489845	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492271	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs499445	1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs501563	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs504026	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs508656	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511469	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516519	0.82[ASN][1000 genomes]
rs527060	0.92[EUR][1000 genomes]
rs537114	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540637	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540714	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541639	1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547516	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs555596	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs571937	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs583680	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs586144	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs598959	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs600186	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609806	0.83[EUR][1000 genomes]
rs612877	0.92[EUR][1000 genomes]
rs627522	0.92[CHB][hapmap]
rs631436	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs651454	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs661453	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102235	0.85[EUR][1000 genomes]
rs8112775	1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs924485	0.92[CHB][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv578950	chr19:21388995-21477431	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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