Variant report

Variant	rs1820505
Chromosome Location	chr4:20717392-20717393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10031524	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938803	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11936560	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940062	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2114474	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322687	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3764965	0.85[EUR][1000 genomes]
rs3816874	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577580	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874299	0.80[EUR][1000 genomes]
rs61428210	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6447971	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447972	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447973	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811933	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6857386	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858843	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7662488	0.81[ASN][1000 genomes]
rs7663837	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7668797	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688592	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689421	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7694208	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs964019	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv3406683	chr4:20714554-20718752	Strong transcription Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3438421	chr4:20716154-20720452	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1820505	PACRGL	cis	lung	GTEx
rs1820505	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs1820505	PACRGL	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20702400-20722600	Weak transcription	Spleen	Spleen
2	chr4:20703000-20717400	Weak transcription	Fetal Heart	heart
3	chr4:20703000-20721800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:20703000-20722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
6	chr4:20703200-20722800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:20703400-20722800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:20703400-20722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:20703400-20723600	Weak transcription	Pancreas	Pancrea
11	chr4:20703400-20724000	Weak transcription	A549	lung
12	chr4:20705000-20718200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:20705400-20718200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:20706000-20717400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:20706600-20722600	Weak transcription	Gastric	stomach
16	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas
17	chr4:20707200-20717400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:20707200-20717400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:20707200-20722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:20707200-20722800	Weak transcription	Thymus	Thymus
21	chr4:20707200-20723200	Weak transcription	Esophagus	oesophagus
22	chr4:20707200-20723400	Weak transcription	Colonic Mucosa	Colon
23	chr4:20707200-20724000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:20707200-20739400	Weak transcription	HepG2	liver
25	chr4:20707400-20722600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:20707600-20717400	Weak transcription	HSMMtube	muscle
27	chr4:20707600-20722200	Weak transcription	Small Intestine	intestine
28	chr4:20707600-20723000	Weak transcription	Right Ventricle	heart
29	chr4:20707600-20724000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:20707600-20724000	Weak transcription	NHEK	skin
31	chr4:20707600-20724000	Weak transcription	NHLF	lung
32	chr4:20708000-20724000	Weak transcription	HMEC	breast
33	chr4:20708200-20733600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:20709400-20717800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:20709400-20722200	Weak transcription	Fetal Thymus	thymus
36	chr4:20709400-20722800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:20709400-20724200	Weak transcription	HUVEC	blood vessel
38	chr4:20709600-20717400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:20709600-20722600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:20709800-20717400	Weak transcription	Brain Anterior Caudate	brain
41	chr4:20711200-20717400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:20711800-20722200	Weak transcription	Placenta	Placenta
43	chr4:20712600-20724000	Weak transcription	HSMM	muscle
44	chr4:20714200-20717800	Strong transcription	Fetal Brain Female	brain
45	chr4:20714200-20718200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:20714400-20718000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:20714400-20718200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:20714400-20718200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:20714400-20718200	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr4:20714400-20718200	Strong transcription	Duodenum Mucosa	Duodenum

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