Variant report

Variant	rs11668752
Chromosome Location	chr19:56094578-56094579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56092829..56094744-chr19:56095214..56096826,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1053817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs11666636	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667786	1.00[ASW][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11669643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671353	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671421	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671545	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902747	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331432	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60547841	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73058305	1.00[ASN][1000 genomes]
rs73058308	1.00[ASN][1000 genomes]
rs73058310	1.00[ASN][1000 genomes]
rs73612853	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100277	1.00[ASN][1000 genomes]
rs8109904	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][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	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11668752	ZNF497	cis	parietal	SCAN
rs11668752	ZNF772	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56092600-56096200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56092600-56097000	Weak transcription	Small Intestine	intestine
3	chr19:56092800-56096200	Weak transcription	Right Ventricle	heart
4	chr19:56092800-56096600	Weak transcription	NH-A	brain
5	chr19:56092800-56096800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:56092800-56096800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:56092800-56096800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:56092800-56096800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:56092800-56097000	Weak transcription	HSMMtube	muscle
10	chr19:56093000-56096800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:56093000-56096800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:56093000-56096800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:56093000-56096800	Weak transcription	Fetal Brain Male	brain
14	chr19:56093000-56096800	Weak transcription	HSMM	muscle
15	chr19:56093000-56097000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:56093000-56097000	Weak transcription	Lung	lung
17	chr19:56093000-56097000	Weak transcription	Ovary	ovary
18	chr19:56093000-56097000	Weak transcription	Right Atrium	heart
19	chr19:56093200-56096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:56093200-56096800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:56093200-56096800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:56093200-56096800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:56093200-56096800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:56093200-56096800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:56093200-56096800	Weak transcription	Fetal Brain Female	brain
26	chr19:56093200-56096800	Weak transcription	Fetal Heart	heart
27	chr19:56093200-56096800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:56093200-56097000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:56093200-56097000	Weak transcription	Left Ventricle	heart
30	chr19:56093200-56097200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr19:56093200-56097200	Weak transcription	Psoas Muscle	Psoas
32	chr19:56093200-56097400	Weak transcription	Gastric	stomach
33	chr19:56093200-56098400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:56093400-56096800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:56093400-56096800	Weak transcription	Brain Anterior Caudate	brain
36	chr19:56093400-56096800	Weak transcription	Brain Germinal Matrix	brain
37	chr19:56093400-56096800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:56093400-56096800	Weak transcription	Fetal Stomach	stomach
39	chr19:56093400-56096800	Weak transcription	Fetal Thymus	thymus
40	chr19:56093400-56096800	Weak transcription	Dnd41	blood
41	chr19:56093400-56096800	Weak transcription	Osteobl	bone
42	chr19:56093400-56097000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:56093400-56097000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:56093400-56097000	Weak transcription	Primary B cells from cord blood	blood
45	chr19:56093400-56097000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:56093400-56097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:56093400-56097400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr19:56093400-56097400	Weak transcription	Stomach Mucosa	stomach
49	chr19:56093400-56097400	Weak transcription	Spleen	Spleen
50	chr19:56093600-56095800	Weak transcription	Hela-S3	cervix

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