Variant report

Variant	rs4854234
Chromosome Location	chr2:95537245-95537246
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:95536957-95537339	ECC-1	luminal epithelium:	n/a	n/a
2	FOXA2	chr2:95536945-95537497	A549	lung:	n/a	n/a
3	MAX	chr2:95537141-95537741	ECC-1	luminal epithelium:	n/a	n/a
4	FOXA2	chr2:95536979-95537466	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:95537210-95537260	HepG2	liver:	n/a
2	chr2:95537210-95537260	MCF-7	breast:	n/a
3	chr2:95537197-95537247	HRE	kidney:	n/a
4	chr2:95537210-95537260	Hela-S3	cervix:	n/a
5	chr2:95537210-95537260	PrEC	prostate:	n/a
6	chr2:95537197-95537247	HL-60	blood:	n/a
7	chr2:95537210-95537260	HEEpiC	esophagus:	n/a
8	chr2:95537197-95537247	A549	lung:	n/a
9	chr2:95537210-95537260	AG04450	lung:	fetal
10	chr2:95537197-95537247	AG09309	skin:	n/a
11	chr2:95537197-95537247	HRCEpiC	kidney:	n/a
12	chr2:95537210-95537260	GM12891	blood:	n/a
13	chr2:95537197-95537247	Hela-S3	cervix:	n/a
14	chr2:95537197-95537247	Caco-2	colon:	n/a
15	chr2:95537210-95537260	ovcar-3	ovarian:	n/a
16	chr2:95537210-95537260	GM12878	blood:	n/a
17	chr2:95537210-95537260	A549	lung:	n/a
18	chr2:95537210-95537260	HEK293	kidney:	embryo
19	chr2:95537210-95537260	RPTEC	kidney:	n/a
20	chr2:95537210-95537260	NHBE	bronchial:	n/a
21	chr2:95537210-95537260	GM06990	blood:	n/a
22	chr2:95537197-95537247	LNCaP	prostate:	n/a
23	chr2:95537197-95537247	HEEpiC	esophagus:	n/a
24	chr2:95537197-95537247	GM12892	blood:	n/a
25	chr2:95537210-95537260	SK-N-SH	brain:	n/a
26	chr2:95537210-95537260	IMR90	lung:	fetal
27	chr2:95537197-95537247	PrEC	prostate:	n/a
28	chr2:95537210-95537260	LNCaP	prostate:	n/a
29	chr2:95537210-95537260	T-47D	breast:	n/a
30	chr2:95537197-95537247	HAEpiC	amniotic membrane:	n/a
31	chr2:95537210-95537260	BJ	skin:	n/a
32	chr2:95537210-95537260	HRCEpiC	kidney:	n/a
33	chr2:95537210-95537260	AG10803	skin:	n/a
34	chr2:95537197-95537247	HEK293	kidney:	embryo
35	chr2:95537210-95537260	HUVEC	blood vessel:	n/a
36	chr2:95537197-95537247	IMR90	lung:	fetal
37	chr2:95537210-95537260	NHDF-neo	bronchial:	n/a
38	chr2:95537197-95537247	PANC-1	pancreas:	n/a
39	chr2:95537210-95537260	K562	blood:	n/a
40	chr2:95537197-95537247	AoSMC	blood vessel:	n/a
41	chr2:95537210-95537260	Hepatocyte	liver:	n/a
42	chr2:95537197-95537247	GM06990	blood:	n/a
43	chr2:95537210-95537260	SK-N-SH_RA	brain:	n/a
44	chr2:95537210-95537260	ECC-1	luminal epithelium:	n/a
45	chr2:95537197-95537247	AG09319	gingival:	n/a
46	chr2:95537197-95537247	ProgFib	skin:	n/a
47	chr2:95537210-95537260	HCM	heart:	n/a
48	chr2:95537210-95537260	SK-N-MC	brain:	n/a
49	chr2:95537210-95537260	HCT-116	colon:	n/a
50	chr2:95537210-95537260	NB4	blood:	n/a

No data

Variant related genes	Relation type
TEKT4	TF binding region
TEKT4	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10165220	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10174668	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10180591	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10874467	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164111	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164112	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11883879	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12612789	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13414018	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2004626	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2077443	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28680439	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34087291	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4854231	0.87[EUR][1000 genomes]
rs4854232	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4854233	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854235	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62146933	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62146942	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2759075	chr2:95358799-95620108	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4854234	AC073464.7	cis	Esophagus Mucosa	GTEx
rs4854234	CYP4F32P	cis	Esophagus Mucosa	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95528200-95537400	Weak transcription	Gastric	stomach
2	chr2:95534200-95549400	Weak transcription	Right Atrium	heart
3	chr2:95536200-95538200	ZNF genes & repeats	Lung	lung
4	chr2:95536400-95537400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:95536400-95537400	Bivalent Enhancer	Adipose Nuclei	Adipose
6	chr2:95536400-95537600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:95536400-95537600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:95536400-95537800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:95536600-95537600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:95536600-95537800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:95536600-95537800	Bivalent Enhancer	Fetal Lung	lung
12	chr2:95536600-95538000	Bivalent Enhancer	Placenta	Placenta
13	chr2:95536800-95537600	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr2:95536800-95537600	Active TSS	HSMM	muscle
15	chr2:95536800-95537800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr2:95536800-95537800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:95536800-95537800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:95537000-95537400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:95537000-95537400	Bivalent Enhancer	Brain Germinal Matrix	brain
20	chr2:95537000-95537400	Active TSS	Fetal Kidney	kidney
21	chr2:95537000-95537400	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr2:95537000-95537600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:95537000-95537600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:95537200-95537400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:95537200-95537400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:95537200-95537400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
27	chr2:95537200-95537400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:95537200-95537400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:95537200-95537400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:95537200-95537400	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
31	chr2:95537200-95537400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr2:95537200-95537400	Bivalent Enhancer	Fetal Brain Female	brain
33	chr2:95537200-95537400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr2:95537200-95537400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr2:95537200-95537400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
36	chr2:95537200-95537400	Bivalent/Poised TSS	A549	lung
37	chr2:95537200-95537600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:95537200-95537600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:95537200-95537600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr2:95537200-95537600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:95537200-95537600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
42	chr2:95537200-95537600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr2:95537200-95537800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:95537200-95537800	Enhancers	Pancreas	Pancrea
45	chr2:95537200-95538400	Bivalent/Poised TSS	Brain Anterior Caudate	brain

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