Variant report

Variant	rs56148414
Chromosome Location	chr19:37324788-37324789
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	chr19:37323948..37326050-chr19:37340760..37342851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197863	Chromatin interaction
ENSG00000251247	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs4806352	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806366	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55661810	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55752123	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995417	1.00[ASN][1000 genomes]
rs56333504	0.90[EUR][1000 genomes]
rs62115567	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62115568	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246310	0.89[EUR][1000 genomes]
rs7249694	0.91[EUR][1000 genomes]
rs73037167	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73037169	0.91[EUR][1000 genomes]
rs73037172	0.91[EUR][1000 genomes]
rs73037195	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039109	0.87[ASN][1000 genomes]
rs8107274	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers 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 miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised 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	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic 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	73 gene(s)	inside rSNPs	diseases
6	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv911650	chr19:37241141-37331614	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers 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	27 gene(s)	inside rSNPs	diseases
16	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
17	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
19	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	esv3354270	chr19:37309161-37364929	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56148414	AC012309.5	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37287400-37327400	ZNF genes & repeats	Liver	Liver
2	chr19:37289200-37327000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr19:37289400-37327600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:37289600-37327400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:37289600-37327400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:37292000-37328400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:37293400-37325600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr19:37293600-37325000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr19:37295000-37327200	ZNF genes & repeats	Fetal Lung	lung
10	chr19:37295600-37324800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr19:37295600-37327200	ZNF genes & repeats	Fetal Brain Female	brain
12	chr19:37298200-37327000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:37298400-37328200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:37299400-37327000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:37300000-37327200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
16	chr19:37303000-37325800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:37303200-37325800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr19:37303200-37327800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:37303200-37327800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:37303200-37328000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:37303400-37325600	ZNF genes & repeats	Fetal Intestine Large	intestine
22	chr19:37303400-37327000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:37303800-37327000	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr19:37304200-37327400	ZNF genes & repeats	Dnd41	blood
25	chr19:37308400-37327400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:37308600-37327200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
27	chr19:37308600-37327600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:37309400-37325800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:37309600-37325200	ZNF genes & repeats	Aorta	Aorta
30	chr19:37310000-37325600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
31	chr19:37311000-37328200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:37312600-37328000	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr19:37313200-37325000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:37315600-37325800	ZNF genes & repeats	Fetal Kidney	kidney
35	chr19:37318000-37325000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
36	chr19:37318000-37327200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
37	chr19:37318200-37324800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
38	chr19:37318200-37325600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
39	chr19:37318200-37325800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:37318200-37325800	ZNF genes & repeats	Brain Hippocampus Middle	brain
41	chr19:37318200-37327000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
42	chr19:37318200-37328200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:37318400-37325800	ZNF genes & repeats	Primary B cells from cord blood	blood
44	chr19:37318400-37325800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
45	chr19:37318400-37327200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:37318600-37325600	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr19:37318600-37325800	ZNF genes & repeats	Brain Anterior Caudate	brain
48	chr19:37319400-37325800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:37319400-37325800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:37319400-37326000	ZNF genes & repeats	Primary T cells from cord blood	blood

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