Variant report

Variant	rs17780009
Chromosome Location	chr19:52873618-52873619
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	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs17780037	0.86[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS 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 miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic 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	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17780009	ZNF677	cis	parietal	SCAN
rs17780009	LOC400713	cis	lesional skin	skin_eQTL
rs17780009	TMC4	cis	cerebellum	SCAN
rs17780009	LOC400713	Cis_1M	lymphoblastoid	RTeQTL
rs17780009	ZNF761	cis	parietal	SCAN
rs17780009	CHMP2A	cis	parietal	SCAN
rs17780009	ZNF160	cis	parietal	SCAN
rs17780009	ZNF880	cis	Artery Tibial	GTEx
rs17780009	LOC400713	cis	uninvolved skin	skin_eQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
3	chr19:52871200-52876400	Weak transcription	Dnd41	blood
4	chr19:52872400-52874000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr19:52872600-52873800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:52872600-52873800	Active TSS	Fetal Brain Female	brain
7	chr19:52872600-52873800	Active TSS	Right Ventricle	heart
8	chr19:52872600-52874000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr19:52872600-52874000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:52872600-52874000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:52872600-52874000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:52872600-52874000	Active TSS	Duodenum Mucosa	Duodenum
13	chr19:52872600-52874000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr19:52872600-52874000	Active TSS	Fetal Intestine Small	intestine
15	chr19:52872600-52874000	Active TSS	Fetal Muscle Trunk	muscle
16	chr19:52872600-52874000	Active TSS	Fetal Muscle Leg	muscle
17	chr19:52872600-52874000	Active TSS	Fetal Stomach	stomach
18	chr19:52872600-52874000	Active TSS	Right Atrium	heart
19	chr19:52872600-52874000	Active TSS	Thymus	Thymus
20	chr19:52872600-52874200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:52872600-52874400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:52872600-52874400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:52872600-52874400	Active TSS	Fetal Kidney	kidney
24	chr19:52872600-52874800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:52872800-52873800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr19:52872800-52873800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr19:52872800-52873800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:52872800-52873800	Active TSS	Aorta	Aorta
29	chr19:52872800-52873800	Active TSS	Brain Angular Gyrus	brain
30	chr19:52872800-52873800	Active TSS	Brain Substantia Nigra	brain
31	chr19:52872800-52873800	Active TSS	Colon Smooth Muscle	Colon
32	chr19:52872800-52873800	Active TSS	Gastric	stomach
33	chr19:52872800-52873800	ZNF genes & repeats	Lung	lung
34	chr19:52872800-52873800	Active TSS	Stomach Mucosa	stomach
35	chr19:52872800-52874000	Active TSS	H1 Cell Line	embryonic stem cell
36	chr19:52872800-52874000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr19:52872800-52874000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:52872800-52874000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:52872800-52874000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr19:52872800-52874000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:52872800-52874000	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr19:52872800-52874000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:52872800-52874000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:52872800-52874000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:52872800-52874000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:52872800-52874000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:52872800-52874000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:52872800-52874000	Active TSS	Brain Anterior Caudate	brain
49	chr19:52872800-52874000	Active TSS	Brain Hippocampus Middle	brain
50	chr19:52872800-52874000	Active TSS	Brain Inferior Temporal Lobe	brain

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