Variant report

Variant	rs62392852
Chromosome Location	chr5:178157115-178157116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr5:178157112-178157932	PANC-1	pancreas:	n/a	n/a
2	MAZ	chr5:178157094-178158170	IMR90	lung:	n/a	chr5:178157954-178157963 chr5:178157203-178157213
3	MAX	chr5:178157106-178158087	A549	lung:	n/a	chr5:178157954-178157963 chr5:178157203-178157213
4	HDAC2	chr5:178157107-178158179	MCF-7	breast:	n/a	n/a
5	ELF1	chr5:178157039-178158042	GM12878	blood:	n/a	chr5:178157429-178157441 chr5:178157727-178157739 chr5:178157200-178157212 chr5:178157635-178157647
6	MAX	chr5:178157092-178158118	A549	lung:	n/a	chr5:178157954-178157963 chr5:178157203-178157213
7	CHD1	chr5:178157084-178158135	IMR90	lung:	n/a	n/a
8	E2F6	chr5:178157098-178158072	A549	lung:	n/a	chr5:178157581-178157590 chr5:178157674-178157684
9	POLR2A	chr5:178157059-178157911	PANC-1	pancreas:	n/a	n/a
10	MAX	chr5:178157104-178158326	MCF-7	breast:	n/a	chr5:178157954-178157963 chr5:178157203-178157213
11	NR2F2	chr5:178157097-178158076	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:178154802..178159439-chr5:178284936..178288781,7	MCF-7	breast:
2	chr5:178042530..178044673-chr5:178156858..178158969,2	MCF-7	breast:
3	chr5:178052822..178055819-chr5:178156143..178158096,2	MCF-7	breast:
4	chr5:178156014..178158845-chr5:178285994..178289826,5	MCF-7	breast:
5	chr5:178049762..178051706-chr5:178156637..178158195,2	MCF-7	breast:
6	chr5:178056292..178058896-chr5:178156268..178158313,2	MCF-7	breast:

Variant related genes	Relation type
ZNF354A	TF binding region
ENSG00000178338	Chromatin interaction
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10043035	0.93[ASN][1000 genomes]
rs11747232	0.92[ASN][1000 genomes]
rs11747390	0.92[ASN][1000 genomes]
rs11750409	0.92[ASN][1000 genomes]
rs13173130	0.93[ASN][1000 genomes]
rs13186580	0.93[ASN][1000 genomes]
rs34601045	0.90[ASN][1000 genomes]
rs34651317	0.92[ASN][1000 genomes]
rs34981407	0.90[ASN][1000 genomes]
rs35007468	0.90[ASN][1000 genomes]
rs35850587	0.92[ASN][1000 genomes]
rs4533908	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4612090	0.82[ASN][1000 genomes]
rs55774261	0.86[ASN][1000 genomes]
rs55818572	0.88[ASN][1000 genomes]
rs56027952	0.88[ASN][1000 genomes]
rs56070635	0.88[ASN][1000 genomes]
rs62392842	0.88[ASN][1000 genomes]
rs62392853	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62392854	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66947564	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6870021	0.85[ASN][1000 genomes]
rs6890741	0.85[ASN][1000 genomes]
rs71611460	0.89[AFR][1000 genomes];0.93[ASN][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
rs62392852	ZNF354A	cis	Thyroid	GTEx

Chromatin state (count:124 , 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	chr5:178152800-178157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:178154000-178157200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:178154200-178157200	Weak transcription	Small Intestine	intestine
5	chr5:178155600-178157200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:178155800-178157800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:178155800-178157800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:178155800-178158200	Active TSS	Muscle Satellite Cultured Cells	--
9	chr5:178156200-178157200	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr5:178156200-178157600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:178156200-178157800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr5:178156200-178157800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:178156200-178157800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr5:178156200-178157800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:178156200-178157800	Active TSS	Fetal Stomach	stomach
16	chr5:178156200-178157800	Active TSS	Lung	lung
17	chr5:178156200-178157800	Active TSS	Stomach Smooth Muscle	stomach
18	chr5:178156200-178158000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr5:178156200-178158000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:178156200-178158000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:178156200-178158000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:178156200-178158000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:178156200-178158000	Active TSS	Esophagus	oesophagus
24	chr5:178156200-178158200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr5:178156400-178157200	Enhancers	Spleen	Spleen
26	chr5:178156400-178157400	Flanking Active TSS	Dnd41	blood
27	chr5:178156400-178157800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:178156400-178157800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:178156400-178157800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:178156400-178157800	Active TSS	Placenta	Placenta
31	chr5:178156400-178157800	Active TSS	Pancreas	Pancrea
32	chr5:178156400-178157800	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr5:178156400-178157800	Active TSS	NH-A	brain
34	chr5:178156400-178157800	Active TSS	NHDF-Ad	bronchial
35	chr5:178156400-178158000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:178156400-178158000	Active TSS	Left Ventricle	heart
37	chr5:178156400-178158000	Active TSS	Psoas Muscle	Psoas
38	chr5:178156400-178158000	Active TSS	Right Ventricle	heart
39	chr5:178156400-178158000	Active TSS	HMEC	breast
40	chr5:178156400-178158000	Active TSS	HSMM	muscle
41	chr5:178156400-178158200	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr5:178156400-178158200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:178156400-178158200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:178156400-178158200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:178156400-178158200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:178156400-178158200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:178156400-178158200	Active TSS	Brain Anterior Caudate	brain
48	chr5:178156400-178158200	Active TSS	Brain Hippocampus Middle	brain
49	chr5:178156400-178158200	Active TSS	Colonic Mucosa	Colon
50	chr5:178156400-178158200	Active TSS	Duodenum Smooth Muscle	Duodenum

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