Variant report

Variant	rs59615456
Chromosome Location	chr4:57180563-57180564
allele	C/G
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	UBTF	chr4:57180345-57180759	K562	blood:	n/a	n/a
2	RCOR1	chr4:57180508-57180738	K562	blood:	n/a	n/a
3	ZNF263	chr4:57180265-57181419	K562	blood:	n/a	chr4:57180750-57180771 chr4:57180783-57180804
4	UBTF	chr4:57180230-57180853	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57175601..57178505-chr4:57178570..57181893,3	K562	blood:

Variant related genes	Relation type
KIAA1211	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10031550	0.86[EUR][1000 genomes]
rs10034154	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11733474	0.83[ASN][1000 genomes]
rs12331363	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12331412	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13114104	0.81[EUR][1000 genomes]
rs13147824	0.80[EUR][1000 genomes]
rs1356788	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1401912	0.81[EUR][1000 genomes]
rs1464286	0.81[EUR][1000 genomes]
rs1976815	0.81[EUR][1000 genomes]
rs1996650	0.81[EUR][1000 genomes]
rs2030365	0.81[EUR][1000 genomes]
rs2139512	0.80[EUR][1000 genomes]
rs28559894	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899063	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3796542	0.81[EUR][1000 genomes]
rs3796547	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822003	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4167	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865087	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865101	0.81[EUR][1000 genomes]
rs57503982	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61750793	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs62310633	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554352	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6554355	0.81[EUR][1000 genomes]
rs6554356	0.81[EUR][1000 genomes]
rs6812041	0.81[EUR][1000 genomes]
rs6826795	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7657711	0.81[EUR][1000 genomes]
rs7661712	0.81[EUR][1000 genomes]
rs7683781	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9683679	0.81[EUR][1000 genomes]
rs9684298	0.81[EUR][1000 genomes]
rs9993277	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9997639	0.81[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59615456	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57162800-57189400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:57163000-57184000	Weak transcription	Right Atrium	heart
3	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
5	chr4:57171000-57187400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
7	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:57173800-57182600	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr4:57173800-57185200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
11	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
12	chr4:57174600-57182200	Weak transcription	HepG2	liver
13	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:57176000-57183400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr4:57176000-57190000	Weak transcription	Gastric	stomach
16	chr4:57176600-57183200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:57177200-57183000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:57177400-57185200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:57177600-57181200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:57177600-57182200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:57177800-57183400	Strong transcription	Colonic Mucosa	Colon
23	chr4:57177800-57184000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:57177800-57184200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:57178000-57190400	Weak transcription	Brain Angular Gyrus	brain
26	chr4:57178200-57183600	Strong transcription	Fetal Stomach	stomach
27	chr4:57178200-57184400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:57178200-57189400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:57178200-57189800	Weak transcription	Brain Anterior Caudate	brain
30	chr4:57178200-57190000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:57178200-57190200	Weak transcription	Brain Substantia Nigra	brain
32	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:57178400-57182800	Weak transcription	Fetal Lung	lung
34	chr4:57178400-57183200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:57178600-57190200	Weak transcription	Fetal Brain Male	brain
36	chr4:57178800-57181000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr4:57178800-57181800	Strong transcription	Fetal Muscle Leg	muscle
38	chr4:57178800-57182200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:57178800-57183200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:57178800-57187000	Strong transcription	Fetal Brain Female	brain
41	chr4:57179000-57180600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:57179000-57183000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:57179200-57182800	Strong transcription	Ovary	ovary
44	chr4:57179200-57183000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:57179200-57186200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:57179400-57181800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:57179400-57183000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:57179600-57181600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr4:57180000-57180800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:57180000-57181200	Strong transcription	Rectal Smooth Muscle	rectum

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