Variant report

Variant	rs4263445
Chromosome Location	chr4:57202377-57202378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10008223	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10010544	0.90[EUR][1000 genomes]
rs10013402	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10017460	0.86[ASN][1000 genomes]
rs10434444	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10434445	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10461357	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060472	0.88[ASN][1000 genomes]
rs1124569	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11723782	0.86[EUR][1000 genomes]
rs12498340	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12501334	0.86[ASN][1000 genomes]
rs12503412	0.86[ASN][1000 genomes]
rs12512742	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1474179	0.81[ASN][1000 genomes]
rs17086696	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1983378	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030366	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2049088	0.85[EUR][1000 genomes]
rs28510634	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28866881	0.86[ASN][1000 genomes]
rs4864579	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864580	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864583	0.86[ASN][1000 genomes]
rs4865088	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865089	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865092	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5010012	0.85[ASN][1000 genomes]
rs56392224	0.86[ASN][1000 genomes]
rs56887793	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58151706	0.85[ASN][1000 genomes]
rs59997251	0.87[EUR][1000 genomes]
rs61032900	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554344	0.86[EUR][1000 genomes]
rs67957495	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6820279	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6820314	0.86[ASN][1000 genomes]
rs6829250	0.86[ASN][1000 genomes]
rs6832797	0.84[ASN][1000 genomes]
rs6834696	0.88[ASN][1000 genomes]
rs7670991	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7696808	0.88[EUR][1000 genomes]
rs8340	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9799864	0.81[AMR][1000 genomes];0.88[ASN][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
rs4263445	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
3	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
4	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
6	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:57181400-57203800	Weak transcription	HSMMtube	muscle
9	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:57187200-57202600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:57188400-57203600	Weak transcription	Fetal Lung	lung
12	chr4:57190400-57203000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:57190400-57203200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:57190400-57203600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
16	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
17	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
18	chr4:57190800-57202600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:57190800-57202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:57190800-57203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:57190800-57203600	Weak transcription	Fetal Brain Male	brain
22	chr4:57190800-57203800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:57191000-57204000	Weak transcription	Brain Angular Gyrus	brain
24	chr4:57193000-57204000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:57193600-57213000	Weak transcription	Left Ventricle	heart
26	chr4:57194800-57202600	Weak transcription	Fetal Stomach	stomach
27	chr4:57194800-57203000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:57195000-57202600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:57195000-57202600	Weak transcription	Fetal Intestine Small	intestine
30	chr4:57195000-57214400	Weak transcription	Placenta	Placenta
31	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
32	chr4:57195400-57203200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:57195800-57203000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:57195800-57203000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:57195800-57203000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:57195800-57203000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:57195800-57203000	Weak transcription	Brain Germinal Matrix	brain
38	chr4:57195800-57203200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:57196000-57202600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:57196000-57202800	Weak transcription	Fetal Brain Female	brain
41	chr4:57196000-57204600	Weak transcription	HSMM	muscle
42	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:57196200-57202600	Weak transcription	Fetal Intestine Large	intestine
44	chr4:57197000-57202800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:57197200-57202600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:57197200-57202600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:57197200-57202600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:57197200-57202800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:57197200-57203200	Weak transcription	Ovary	ovary
50	chr4:57197200-57203800	Weak transcription	Rectal Mucosa Donor 31	rectum

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