Variant report

Variant	rs12974540
Chromosome Location	chr19:57007444-57007445
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:57002795..57005630-chr19:57006374..57008169,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10404345	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10404523	0.86[JPT][hapmap]
rs10408147	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408921	0.86[JPT][hapmap]
rs10413986	0.85[JPT][hapmap]
rs10423274	0.86[JPT][hapmap]
rs10426952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17273400	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17273407	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35558315	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35967838	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760848	0.86[JPT][hapmap]
rs60141587	0.83[AFR][1000 genomes]
rs8112950	0.85[JPT][hapmap]
rs877394	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877395	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56990800-57010000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:56992000-57009400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
3	chr19:56992000-57009800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:56998600-57008800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:57003000-57018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:57003200-57018400	Weak transcription	Osteobl	bone
7	chr19:57003600-57017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:57003800-57011600	Weak transcription	Fetal Heart	heart
9	chr19:57004400-57008800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:57004600-57009400	ZNF genes & repeats	Ovary	ovary
11	chr19:57004600-57009600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:57004800-57007800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr19:57004800-57007800	Strong transcription	Right Ventricle	heart
14	chr19:57005200-57008000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:57005400-57007600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr19:57005400-57007800	ZNF genes & repeats	Adipose Nuclei	Adipose
17	chr19:57005400-57007800	Strong transcription	Left Ventricle	heart
18	chr19:57005400-57008400	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:57005400-57008400	ZNF genes & repeats	Spleen	Spleen
20	chr19:57005400-57008600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:57005400-57009000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:57005400-57009200	ZNF genes & repeats	Aorta	Aorta
23	chr19:57005400-57010000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:57005600-57008000	ZNF genes & repeats	Fetal Lung	lung
25	chr19:57005600-57009600	Strong transcription	Brain Anterior Caudate	brain
26	chr19:57005800-57007800	Strong transcription	Brain Germinal Matrix	brain
27	chr19:57005800-57008000	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr19:57006000-57007600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:57006200-57007800	ZNF genes & repeats	Liver	Liver
30	chr19:57006200-57008000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr19:57006200-57018600	Weak transcription	Dnd41	blood
32	chr19:57006400-57007800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
33	chr19:57006400-57007800	Strong transcription	Fetal Kidney	kidney
34	chr19:57006600-57007600	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:57006600-57007600	Strong transcription	Fetal Brain Female	brain
36	chr19:57006600-57007600	ZNF genes & repeats	Thymus	Thymus
37	chr19:57006600-57007800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr19:57006600-57008000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:57006600-57009000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:57006600-57009400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
41	chr19:57006600-57009800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:57006800-57007600	Strong transcription	Fetal Brain Male	brain
43	chr19:57006800-57007800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:57006800-57007800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:57006800-57007800	ZNF genes & repeats	Brain Hippocampus Middle	brain
46	chr19:57006800-57007800	ZNF genes & repeats	Esophagus	oesophagus
47	chr19:57006800-57007800	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr19:57006800-57007800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:57006800-57008000	ZNF genes & repeats	Brain Substantia Nigra	brain
50	chr19:57006800-57008000	ZNF genes & repeats	Rectal Smooth Muscle	rectum

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