Variant report

Variant	rs4612090
Chromosome Location	chr5:178156622-178156623
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178154802..178159439-chr5:178284936..178288781,7	MCF-7	breast:
2	chr5:178052822..178055819-chr5:178156143..178158096,2	MCF-7	breast:
3	chr5:178156014..178158845-chr5:178285994..178289826,5	MCF-7	breast:
4	chr5:178056292..178058896-chr5:178156268..178158313,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction
ENSG00000178338	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10043035	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11747232	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11747390	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11750409	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13173130	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13186580	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34601045	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34651317	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34981407	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35007468	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35287913	0.81[AMR][1000 genomes]
rs35850587	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4533908	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56328282	0.84[AMR][1000 genomes]
rs62392851	0.82[AMR][1000 genomes]
rs62392852	0.82[ASN][1000 genomes]
rs62392853	0.82[AFR][1000 genomes]
rs62392854	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66947564	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71611460	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4612090	ZNF354A	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178149400-178164400	Weak transcription	Fetal Heart	heart
2	chr5:178149800-178157000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:178150000-178156800	Weak transcription	HUVEC	blood vessel
4	chr5:178150800-178156800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:178152800-178157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:178154000-178157200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:178154200-178156800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:178154200-178156800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:178154200-178157000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:178154200-178157000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:178154200-178157200	Weak transcription	Small Intestine	intestine
12	chr5:178154800-178156800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:178154800-178156800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:178155000-178156800	Weak transcription	Fetal Lung	lung
15	chr5:178155000-178157000	Weak transcription	Ovary	ovary
16	chr5:178155200-178157000	Weak transcription	Aorta	Aorta
17	chr5:178155400-178156800	Weak transcription	Primary B cells from cord blood	blood
18	chr5:178155400-178156800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr5:178155400-178156800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:178155400-178157000	Weak transcription	A549	lung
21	chr5:178155600-178156800	Weak transcription	Liver	Liver
22	chr5:178155600-178157200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:178155800-178157800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:178155800-178157800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:178155800-178158200	Active TSS	Muscle Satellite Cultured Cells	--
26	chr5:178156200-178156800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:178156200-178156800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:178156200-178157200	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr5:178156200-178157600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:178156200-178157800	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr5:178156200-178157800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:178156200-178157800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr5:178156200-178157800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:178156200-178157800	Active TSS	Fetal Stomach	stomach
35	chr5:178156200-178157800	Active TSS	Lung	lung
36	chr5:178156200-178157800	Active TSS	Stomach Smooth Muscle	stomach
37	chr5:178156200-178158000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr5:178156200-178158000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:178156200-178158000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:178156200-178158000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:178156200-178158000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:178156200-178158000	Active TSS	Esophagus	oesophagus
43	chr5:178156200-178158200	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr5:178156400-178156800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr5:178156400-178156800	Enhancers	Fetal Brain Male	brain
46	chr5:178156400-178157200	Enhancers	Spleen	Spleen
47	chr5:178156400-178157400	Flanking Active TSS	Dnd41	blood
48	chr5:178156400-178157800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:178156400-178157800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:178156400-178157800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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