Variant report

Variant	rs9993277
Chromosome Location	chr4:57174134-57174135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr4:57173261-57174231	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr4:57173403-57174183	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr4:57173316-57174217	ECC-1	luminal epithelium:	n/a	n/a
4	ESR1	chr4:57173361-57174164	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr4:57173222-57174243	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr4:57172846-57174359	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr4:57173447-57174177	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr4:57173347-57174156	ECC-1	luminal epithelium:	n/a	n/a
9	FOXM1	chr4:57173292-57174202	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr4:57173331-57174145	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr4:57173277-57174193	ECC-1	luminal epithelium:	n/a	n/a
12	ESR1	chr4:57173453-57174195	ECC-1	luminal epithelium:	n/a	n/a

No data

Variant related genes	Relation type
KIAA1211	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10034154	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12331363	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12331412	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13147824	0.82[CEU][hapmap]
rs1356788	0.81[EUR][1000 genomes]
rs1401912	0.83[CEU][hapmap]
rs2139512	0.82[CEU][hapmap]
rs28559894	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2899063	0.83[CEU][hapmap]
rs3796547	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3822003	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs4167	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4865087	0.80[EUR][1000 genomes]
rs57503982	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59615456	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62310633	0.90[EUR][1000 genomes]
rs6554349	0.83[CEU][hapmap]
rs6554355	0.83[CEU][hapmap]
rs6554356	0.83[CEU][hapmap]
rs7683781	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7692385	0.83[CEU][hapmap]
rs9683679	0.83[CEU][hapmap]
rs9684298	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9993277	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs9993277	AASDH	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57149400-57179400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:57156800-57177800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:57162800-57189400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:57163000-57177800	Weak transcription	Colonic Mucosa	Colon
5	chr4:57163000-57184000	Weak transcription	Right Atrium	heart
6	chr4:57163400-57180400	Weak transcription	Pancreas	Pancrea
7	chr4:57167600-57179600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:57167800-57174200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:57167800-57176200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:57167800-57176600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:57167800-57177000	Weak transcription	Brain Substantia Nigra	brain
13	chr4:57167800-57178800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:57167800-57179000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
16	chr4:57168000-57177000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:57168400-57179600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:57168600-57179200	Weak transcription	Ovary	ovary
19	chr4:57170000-57176000	Weak transcription	Fetal Brain Male	brain
20	chr4:57170200-57176600	Weak transcription	Fetal Lung	lung
21	chr4:57170400-57176400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:57171000-57187400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:57171200-57174200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:57171400-57174400	Genic enhancers	Fetal Intestine Small	intestine
25	chr4:57171800-57176400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:57172000-57174400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:57172000-57176400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:57172000-57180000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
30	chr4:57172600-57179800	Weak transcription	Placenta	Placenta
31	chr4:57172600-57180000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:57172800-57174600	Genic enhancers	Fetal Intestine Large	intestine
33	chr4:57173000-57174400	Enhancers	HMEC	breast
34	chr4:57173000-57174800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:57173000-57180200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:57173400-57174400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:57173400-57174600	Genic enhancers	Duodenum Mucosa	Duodenum
39	chr4:57173400-57175200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:57173600-57174400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:57173600-57174400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:57173600-57174600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:57173600-57174600	Strong transcription	Fetal Muscle Leg	muscle
44	chr4:57173600-57175000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:57173600-57175800	Strong transcription	Fetal Stomach	stomach
46	chr4:57173600-57176200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:57173600-57180000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:57173800-57174400	Strong transcription	Fetal Kidney	kidney
49	chr4:57173800-57175800	Strong transcription	Fetal Brain Female	brain
50	chr4:57173800-57177600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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