Variant report

Variant	rs66947564
Chromosome Location	chr5:178157809-178157810
allele	A/C
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	POLR2A	chr5:178157413-178157920	K562	blood:	n/a	n/a
2	CTCF	chr5:178157575-178158037	K562	blood:	n/a	chr5:178157986-178157993
3	GTF2F1	chr5:178157569-178157967	Hela-S3	cervix:	n/a	n/a
4	ELK1	chr5:178157654-178157930	K562	blood:	n/a	n/a
5	CTCF	chr5:178157720-178157870	WI-38	lung:	n/a	n/a
6	CTCF	chr5:178157760-178157910	HRPEpiC	eye:	n/a	n/a
7	CTCF	chr5:178157154-178158330	SK-N-SH	brain:	n/a	chr5:178157518-178157536 chr5:178157520-178157533 chr5:178157986-178157993
8	CTCF	chr5:178157507-178158165	MCF-7	breast:	n/a	chr5:178157518-178157536 chr5:178157520-178157533 chr5:178157986-178157993
9	POLR2A	chr5:178157370-178157926	SK-N-SH	brain:	n/a	n/a
10	SIN3AK20	chr5:178157112-178157932	PANC-1	pancreas:	n/a	n/a
11	ZNF384	chr5:178157594-178158032	K562	blood:	n/a	n/a
12	POLR2A	chr5:178157299-178157950	HUVEC	blood vessel:	n/a	n/a
13	GTF2F1	chr5:178157564-178157862	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr5:178157517-178157820	SK-N-SH	brain:	n/a	n/a
15	PAX5	chr5:178157585-178157963	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:178157331-178157964	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:178157420-178157822	Hela-S3	cervix:	n/a	n/a
18	SPI1	chr5:178157659-178157942	GM12878	blood:	n/a	n/a
19	EGR1	chr5:178157732-178158130	K562	blood:	n/a	chr5:178157955-178157964 chr5:178157762-178157786 chr5:178157952-178157965 chr5:178157953-178157964 chr5:178157951-178157966 chr5:178157954-178157964 chr5:178157948-178157970 chr5:178157952-178157966 chr5:178157954-178157964 chr5:178157952-178157965 chr5:178157952-178157965 chr5:178157953-178157964 chr5:178157952-178157965
20	CTCF	chr5:178157760-178157910	GM12872	blood:	n/a	n/a
21	YY1	chr5:178157503-178158002	SK-N-SH_RA	brain:	n/a	chr5:178157515-178157524 chr5:178157587-178157598
22	KAP1	chr5:178157554-178158178	U2OS	brain:	n/a	n/a
23	TCF3	chr5:178157495-178157905	GM12878	blood:	n/a	chr5:178157757-178157771
24	CTCF	chr5:178157704-178157957	MCF-7	breast:	n/a	n/a
25	MXI1	chr5:178157421-178157974	HepG2	liver:	n/a	n/a
26	MAZ	chr5:178157604-178157992	HepG2	liver:	n/a	chr5:178157954-178157963
27	CTCF	chr5:178157617-178158008	SK-N-SH_RA	brain:	n/a	chr5:178157986-178157993
28	RCOR1	chr5:178157617-178157932	HepG2	liver:	n/a	n/a
29	HCFC1	chr5:178157468-178158045	K562	blood:	n/a	n/a
30	SIX5	chr5:178157550-178158180	A549	lung:	n/a	chr5:178157773-178157787 chr5:178157776-178157785 chr5:178157774-178157783
31	RAD21	chr5:178157358-178158055	H1-hESC	embryonic stem cell:	n/a	chr5:178157488-178157502 chr5:178157833-178157852 chr5:178157834-178157848 chr5:178157837-178157846
32	CTCF	chr5:178157760-178157910	HAc	cerebellar:	n/a	n/a
33	CTCF	chr5:178157650-178157962	HepG2	liver:	n/a	n/a
34	MAX	chr5:178157485-178158005	A549	lung:	n/a	chr5:178157954-178157963
35	YY1	chr5:178157535-178158010	GM12892	blood:	n/a	chr5:178157587-178157598
36	NR2F2	chr5:178157538-178157926	K562	blood:	n/a	n/a
37	CTCF	chr5:178157740-178157890	GM12869	blood:	n/a	n/a
38	YY1	chr5:178157514-178157942	HCT-116	colon:	n/a	chr5:178157515-178157524 chr5:178157587-178157598
39	CTCF	chr5:178157760-178157910	K562	blood:	n/a	n/a
40	CTCF	chr5:178157760-178157910	HMEC	breast:	n/a	n/a
41	CTCF	chr5:178157720-178157870	GM12866	blood:	n/a	n/a
42	NFIC	chr5:178157548-178157881	HepG2	liver:	n/a	n/a
43	MXI1	chr5:178157515-178157932	H1-hESC	embryonic stem cell:	n/a	n/a
44	FOXA2	chr5:178157560-178158086	A549	lung:	n/a	n/a
45	CTCF	chr5:178157760-178157910	NHEK	skin:	n/a	n/a
46	EGR1	chr5:178157605-178158272	MCF-7	breast:	n/a	chr5:178157955-178157964 chr5:178157762-178157786 chr5:178157952-178157965 chr5:178157953-178157964 chr5:178157951-178157966 chr5:178157954-178157964 chr5:178157948-178157970 chr5:178157952-178157966 chr5:178157954-178157964 chr5:178158235-178158244 chr5:178157952-178157965 chr5:178157727-178157751 chr5:178157952-178157965 chr5:178157953-178157964 chr5:178157952-178157965
47	POLR2A	chr5:178157475-178157851	GM12878	blood:	n/a	n/a
48	CTCF	chr5:178157760-178157910	AG10803	skin:	n/a	n/a
49	SIX5	chr5:178157515-178157959	A549	lung:	n/a	chr5:178157773-178157787 chr5:178157776-178157785 chr5:178157774-178157783
50	MXI1	chr5:178157292-178157997	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:178157792-178157842	LNCaP	prostate:	n/a
2	chr5:178157801-178157851	K562	blood:	n/a
3	chr5:178157801-178157851	GM12878	blood:	n/a
4	chr5:178157772-178157822	PANC-1	pancreas:	n/a
5	chr5:178157801-178157851	A549	lung:	n/a
6	chr5:178157792-178157842	NH-A	brain:	n/a
7	chr5:178157772-178157822	NB4	blood:	n/a
8	chr5:178157792-178157842	PrEC	prostate:	n/a
9	chr5:178157801-178157851	NB4	blood:	n/a
10	chr5:178157809-178157859	GM12878	blood:	n/a
11	chr5:178157772-178157822	GM12892	blood:	n/a
12	chr5:178157801-178157851	HMEC	breast:	n/a
13	chr5:178157772-178157822	K562	blood:	n/a
14	chr5:178157772-178157822	HRPEpiC	eye:	n/a
15	chr5:178157772-178157822	HCM	heart:	n/a
16	chr5:178157809-178157859	Hela-S3	cervix:	n/a
17	chr5:178157772-178157822	AG09319	gingival:	n/a
18	chr5:178157792-178157842	HNPCEpiC	eye:	n/a
19	chr5:178157809-178157859	AG04450	lung:	fetal
20	chr5:178157809-178157859	HepG2	liver:	n/a
21	chr5:178157801-178157851	HL-60	blood:	n/a
22	chr5:178157809-178157859	T-47D	breast:	n/a
23	chr5:178157801-178157851	AoSMC	blood vessel:	n/a
24	chr5:178157801-178157851	AG09309	skin:	n/a
25	chr5:178157801-178157851	NT2-D1	testis:	n/a
26	chr5:178157792-178157842	AG04450	lung:	fetal
27	chr5:178157809-178157859	HEK293	kidney:	embryo
28	chr5:178157809-178157859	BE2_C	brain:	n/a
29	chr5:178157792-178157842	SK-N-MC	brain:	n/a
30	chr5:178157801-178157851	HCM	heart:	n/a
31	chr5:178157809-178157859	ovcar-3	ovarian:	n/a
32	chr5:178157801-178157851	Jurkat	blood:	n/a
33	chr5:178157772-178157822	HEEpiC	esophagus:	n/a
34	chr5:178157792-178157842	ovcar-3	ovarian:	n/a
35	chr5:178157801-178157851	HNPCEpiC	eye:	n/a
36	chr5:178157792-178157842	HRCEpiC	kidney:	n/a
37	chr5:178157801-178157851	GM06990	blood:	n/a
38	chr5:178157792-178157842	GM12878	blood:	n/a
39	chr5:178157801-178157851	BJ	skin:	n/a
40	chr5:178157792-178157842	SAEC	small airway:	n/a
41	chr5:178157801-178157851	HPAEpiC	pulmonary alveolar:	n/a
42	chr5:178157809-178157859	SAEC	small airway:	n/a
43	chr5:178157772-178157822	AG09309	skin:	n/a
44	chr5:178157801-178157851	SK-N-SH_RA	brain:	n/a
45	chr5:178157792-178157842	PANC-1	pancreas:	n/a
46	chr5:178157801-178157851	NH-A	brain:	n/a
47	chr5:178157772-178157822	GM12878	blood:	n/a
48	chr5:178157772-178157822	AG10803	skin:	n/a
49	chr5:178157801-178157851	GM12891	blood:	n/a
50	chr5:178157772-178157822	ovcar-3	ovarian:	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	chr5:178051446..178054153-chr5:178157357..178158910,2	MCF-7	breast:
5	chr5:178156014..178158845-chr5:178285994..178289826,5	MCF-7	breast:
6	chr5:178157230..178157844-chr5:178286636..178287441,3	MCF-7	breast:
7	chr5:178049762..178051706-chr5:178156637..178158195,2	MCF-7	breast:
8	chr5:178157243..178158078-chr5:178286943..178287443,2	MCF-7	breast:
9	chr5:178056292..178058896-chr5:178156268..178158313,2	MCF-7	breast:

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

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10043035	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1071881	0.84[EUR][1000 genomes]
rs1071882	0.83[EUR][1000 genomes]
rs1071883	0.84[EUR][1000 genomes]
rs1079487	0.84[EUR][1000 genomes]
rs11249566	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1132336	0.84[EUR][1000 genomes]
rs11740283	0.84[EUR][1000 genomes]
rs11742156	0.83[EUR][1000 genomes]
rs11742176	0.84[EUR][1000 genomes]
rs11747097	0.84[EUR][1000 genomes]
rs11747232	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11747390	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11750409	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11750784	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13167549	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13173130	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13186580	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34601045	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34645905	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34651317	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34703961	0.84[EUR][1000 genomes]
rs34981407	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35007468	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35579651	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35850587	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4266420	0.84[EUR][1000 genomes]
rs4533908	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4612090	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55774261	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55818572	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55912234	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55974982	0.84[EUR][1000 genomes]
rs56027952	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56070635	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56236920	0.84[EUR][1000 genomes]
rs59259518	0.84[EUR][1000 genomes]
rs62392839	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62392842	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62392852	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392853	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62392854	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6870021	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6890741	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6896799	0.84[EUR][1000 genomes]
rs71611460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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
rs66947564	ZNF354A	cis	Thyroid	GTEx

Chromatin state (count:115 , 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	chr5:178155800-178158200	Active TSS	Muscle Satellite Cultured Cells	--
3	chr5:178156200-178158000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr5:178156200-178158000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:178156200-178158000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:178156200-178158000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:178156200-178158000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:178156200-178158000	Active TSS	Esophagus	oesophagus
9	chr5:178156200-178158200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:178156400-178158000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:178156400-178158000	Active TSS	Left Ventricle	heart
12	chr5:178156400-178158000	Active TSS	Psoas Muscle	Psoas
13	chr5:178156400-178158000	Active TSS	Right Ventricle	heart
14	chr5:178156400-178158000	Active TSS	HMEC	breast
15	chr5:178156400-178158000	Active TSS	HSMM	muscle
16	chr5:178156400-178158200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr5:178156400-178158200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:178156400-178158200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:178156400-178158200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:178156400-178158200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:178156400-178158200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:178156400-178158200	Active TSS	Brain Anterior Caudate	brain
23	chr5:178156400-178158200	Active TSS	Brain Hippocampus Middle	brain
24	chr5:178156400-178158200	Active TSS	Colonic Mucosa	Colon
25	chr5:178156400-178158200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr5:178156400-178158200	Active TSS	Right Atrium	heart
27	chr5:178156400-178158200	Active TSS	Osteobl	bone
28	chr5:178156600-178158000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr5:178156600-178158000	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr5:178156600-178158000	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr5:178156600-178158000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr5:178156600-178158000	Active TSS	Colon Smooth Muscle	Colon
33	chr5:178156600-178158000	Active TSS	Fetal Brain Female	brain
34	chr5:178156600-178158000	Active TSS	Fetal Kidney	kidney
35	chr5:178156600-178158000	Active TSS	GM12878-XiMat	blood
36	chr5:178156600-178158200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:178156600-178158200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:178156600-178158200	Active TSS	Brain Germinal Matrix	brain
39	chr5:178156600-178158200	Active TSS	Rectal Smooth Muscle	rectum
40	chr5:178156600-178158200	Active TSS	Thymus	Thymus
41	chr5:178156600-178158200	Active TSS	NHLF	lung
42	chr5:178156800-178158000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:178156800-178158000	Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr5:178156800-178158000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:178156800-178158000	Active TSS	Brain Substantia Nigra	brain
46	chr5:178156800-178158000	Weak transcription	Fetal Brain Male	brain
47	chr5:178156800-178158000	Active TSS	Gastric	stomach
48	chr5:178156800-178158000	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr5:178157000-178158000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr5:178157000-178158000	Active TSS	Primary T killer memory cells from peripheral blood	blood

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