Variant report

Variant	rs609806
Chromosome Location	chr19:21512949-21512950
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	chr19:21510924..21513197-chr19:21688433..21691004,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197013	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1114305	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1875256	0.90[ASN][1000 genomes]
rs2086319	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2434996	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2562402	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562409	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562415	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562438	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650797	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2650798	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2650842	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2650849	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2650851	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs279804	0.83[EUR][1000 genomes]
rs279805	0.83[EUR][1000 genomes]
rs279810	0.83[EUR][1000 genomes]
rs279811	0.83[EUR][1000 genomes]
rs279812	0.83[EUR][1000 genomes]
rs279814	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs279815	0.83[EUR][1000 genomes]
rs279816	0.83[EUR][1000 genomes]
rs279820	0.83[EUR][1000 genomes]
rs28771683	0.83[ASN][1000 genomes]
rs2914626	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2914627	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2914635	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2914645	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2928188	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2928209	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2928211	0.88[ASN][1000 genomes]
rs2928216	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2928218	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2937157	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2937174	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968022	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968023	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968024	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968040	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2968041	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968045	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968046	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968066	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2968082	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2968086	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472472	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs475162	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs476376	0.83[EUR][1000 genomes]
rs478046	0.83[EUR][1000 genomes]
rs487991	0.90[EUR][1000 genomes]
rs489613	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs489845	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs492271	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501563	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs504026	0.83[EUR][1000 genomes]
rs508656	0.83[EUR][1000 genomes]
rs511469	0.83[EUR][1000 genomes]
rs516519	0.83[ASN][1000 genomes]
rs527060	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537114	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs540637	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs540714	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs541639	0.83[EUR][1000 genomes]
rs547516	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs555596	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs583680	0.83[EUR][1000 genomes]
rs586144	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs598959	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs600186	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs612877	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627522	0.89[ASN][1000 genomes]
rs631436	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs651454	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs661453	0.83[EUR][1000 genomes]
rs8102235	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8112775	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs924485	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers 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	31 gene(s)	inside rSNPs	diseases
10	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3415719	chr19:21511760-21519079	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21512400-21513200	Flanking Active TSS	Dnd41	blood
2	chr19:21512400-21513600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:21512400-21513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:21512400-21515000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:21512600-21513000	Enhancers	Primary B cells from cord blood	blood
6	chr19:21512600-21513000	Enhancers	Primary B cells from peripheral blood	blood
7	chr19:21512600-21513000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr19:21512600-21513000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr19:21512600-21513000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:21512600-21513000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:21512600-21513200	Enhancers	Primary T helper cells fromperipheralblood	blood

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