Variant report

Variant	rs28544429
Chromosome Location	chr4:8506081-8506082
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	EP300	chr4:8505779-8506732	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr4:8506080-8506230	SK-N-SH_RA	brain:	n/a	n/a
3	TCF12	chr4:8505789-8506674	ECC-1	luminal epithelium:	n/a	chr4:8506122-8506132
4	ESR1	chr4:8506032-8506400	ECC-1	luminal epithelium:	n/a	n/a
5	TEAD4	chr4:8505900-8506485	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr4:8505830-8506588	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr4:8505876-8506726	ECC-1	luminal epithelium:	n/a	chr4:8506122-8506132
8	ZNF263	chr4:8505867-8506432	HEK293-T-REx	kidney:	n/a	chr4:8506130-8506139 chr4:8506088-8506109
9	NFIC	chr4:8505464-8506730	ECC-1	luminal epithelium:	n/a	n/a
10	ESR1	chr4:8506010-8506799	ECC-1	luminal epithelium:	n/a	n/a
11	TEAD4	chr4:8505929-8506595	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr4:8505989-8506465	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr4:8505812-8506752	ECC-1	luminal epithelium:	n/a	n/a
14	YY1	chr4:8505935-8506468	ECC-1	luminal epithelium:	n/a	n/a
15	RAD21	chr4:8506003-8506368	ECC-1	luminal epithelium:	n/a	chr4:8506167-8506181
16	ZBTB7A	chr4:8505844-8506769	ECC-1	luminal epithelium:	n/a	n/a
17	NR3C1	chr4:8506022-8506388	ECC-1	luminal epithelium:	n/a	n/a
18	ESR1	chr4:8505960-8506815	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8500499..8503047-chr4:8505239..8508077,2	K562	blood:
2	chr4:8499417..8502342-chr4:8505170..8507298,2	MCF-7	breast:
3	chr4:8479557..8483754-chr4:8505033..8507334,3	K562	blood:

Variant related genes	Relation type
ENSG00000205959	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10008186	0.85[EUR][1000 genomes]
rs10009833	0.81[EUR][1000 genomes]
rs10012186	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10015429	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10029016	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10031818	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10938715	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11736150	0.92[EUR][1000 genomes]
rs11934642	0.81[EUR][1000 genomes]
rs13105919	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842416	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28536709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28739492	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2972	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
3	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3377450	chr4:8502852-8506150	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv4224	chr4:8503727-8546462	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8501600-8507000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:8501600-8507000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:8501600-8507400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:8501600-8507400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:8501600-8507600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:8501600-8507600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:8501600-8507600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:8501600-8507800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:8501600-8507800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:8501600-8507800	Weak transcription	Brain Angular Gyrus	brain
11	chr4:8501800-8510600	Enhancers	Ovary	ovary
12	chr4:8502800-8512800	Enhancers	Placenta	Placenta
13	chr4:8503000-8506800	Enhancers	Brain Hippocampus Middle	brain
14	chr4:8503600-8509400	Enhancers	Right Ventricle	heart
15	chr4:8503600-8509800	Enhancers	Adipose Nuclei	Adipose
16	chr4:8504000-8506200	Enhancers	Fetal Heart	heart
17	chr4:8504200-8506200	Enhancers	Fetal Brain Male	brain
18	chr4:8504200-8506400	Enhancers	Left Ventricle	heart
19	chr4:8504200-8506400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr4:8504200-8506600	Enhancers	Pancreas	Pancrea
21	chr4:8504200-8509000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr4:8504200-8509400	Enhancers	Right Atrium	heart
23	chr4:8504200-8510600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:8504400-8506200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:8504400-8506400	Enhancers	Lung	lung
26	chr4:8504400-8506600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr4:8504400-8507400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr4:8504600-8506400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr4:8504600-8507200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:8504600-8507600	Weak transcription	Fetal Kidney	kidney
31	chr4:8504600-8510800	Enhancers	Fetal Muscle Leg	muscle
32	chr4:8504800-8506200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr4:8504800-8506200	Weak transcription	HSMMtube	muscle
34	chr4:8504800-8507800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:8505000-8508000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr4:8505200-8506400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:8505200-8506400	Enhancers	Brain Substantia Nigra	brain
38	chr4:8505200-8506400	Enhancers	Fetal Brain Female	brain
39	chr4:8505200-8507800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:8505200-8507800	Weak transcription	Brain Anterior Caudate	brain
41	chr4:8505200-8508000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:8505400-8506200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:8505400-8507800	Weak transcription	HSMM	muscle
44	chr4:8505400-8509000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:8505600-8506200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:8505600-8506200	Enhancers	Gastric	stomach
47	chr4:8505600-8506200	Bivalent Enhancer	HMEC	breast
48	chr4:8505600-8507800	Weak transcription	NHDF-Ad	bronchial
49	chr4:8505800-8506200	Enhancers	Colonic Mucosa	Colon
50	chr4:8505800-8506200	Enhancers	Duodenum Smooth Muscle	Duodenum

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