Variant report

Variant	rs4577580
Chromosome Location	chr4:20720532-20720533
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10031524	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938803	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11936560	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940062	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820505	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114474	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322687	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3816874	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61428210	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6447971	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447972	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447973	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811933	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6857386	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858843	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7662488	0.81[ASN][1000 genomes]
rs7663837	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7668797	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688592	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689421	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7694208	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs964019	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4577580	PACRGL	cis	Thyroid	GTEx
rs4577580	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs4577580	PACRGL	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20702400-20722600	Weak transcription	Spleen	Spleen
2	chr4:20703000-20721800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:20703000-20722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
5	chr4:20703200-20722800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:20703400-20722800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:20703400-20722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:20703400-20723600	Weak transcription	Pancreas	Pancrea
10	chr4:20703400-20724000	Weak transcription	A549	lung
11	chr4:20706600-20722600	Weak transcription	Gastric	stomach
12	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas
13	chr4:20707200-20722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:20707200-20722800	Weak transcription	Thymus	Thymus
15	chr4:20707200-20723200	Weak transcription	Esophagus	oesophagus
16	chr4:20707200-20723400	Weak transcription	Colonic Mucosa	Colon
17	chr4:20707200-20724000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:20707200-20739400	Weak transcription	HepG2	liver
19	chr4:20707400-20722600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:20707600-20722200	Weak transcription	Small Intestine	intestine
21	chr4:20707600-20723000	Weak transcription	Right Ventricle	heart
22	chr4:20707600-20724000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr4:20707600-20724000	Weak transcription	NHEK	skin
24	chr4:20707600-20724000	Weak transcription	NHLF	lung
25	chr4:20708000-20724000	Weak transcription	HMEC	breast
26	chr4:20708200-20733600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:20709400-20722200	Weak transcription	Fetal Thymus	thymus
28	chr4:20709400-20722800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:20709400-20724200	Weak transcription	HUVEC	blood vessel
30	chr4:20709600-20722600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:20711800-20722200	Weak transcription	Placenta	Placenta
32	chr4:20712600-20724000	Weak transcription	HSMM	muscle
33	chr4:20715000-20723600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:20715200-20722400	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:20715200-20724000	Weak transcription	Primary B cells from cord blood	blood
36	chr4:20715200-20724000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:20715400-20721800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:20715400-20722200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:20715400-20724000	Weak transcription	K562	blood
40	chr4:20715400-20738600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:20715400-20739400	Weak transcription	Osteobl	bone
42	chr4:20717600-20722200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:20717600-20722800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:20717800-20722800	Weak transcription	Fetal Intestine Small	intestine
45	chr4:20717800-20724200	Weak transcription	NH-A	brain
46	chr4:20718000-20721800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:20718000-20721800	Weak transcription	Liver	Liver
48	chr4:20718000-20722000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:20718000-20722200	Weak transcription	Brain Anterior Caudate	brain
50	chr4:20718000-20722600	Weak transcription	Brain Substantia Nigra	brain

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