Variant report

Variant	rs58367397
Chromosome Location	chr3:121451700-121451701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121451393..121453533-chr3:121465182..121467129,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10049060	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1127412	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1128163	0.82[EUR][1000 genomes]
rs11916169	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11928871	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12634032	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12635865	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1463736	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1574115	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1574133	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141487	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3732407	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3732410	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772126	0.85[EUR][1000 genomes]
rs4048699	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4048703	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6771068	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6775822	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6791882	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7153	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7610298	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7623901	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7647351	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7648340	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7648343	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9808981	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9817818	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818073	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9820511	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9823335	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9824235	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824760	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838301	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9850439	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9852845	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9874722	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs58367397	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs58367397	STAM2	trans	lymphoblastoid	RTeQTL
rs58367397	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs58367397	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs58367397	EAF2	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121436600-121466600	Weak transcription	Stomach Mucosa	stomach
2	chr3:121439400-121467200	Weak transcription	Small Intestine	intestine
3	chr3:121443400-121464800	Weak transcription	Fetal Brain Male	brain
4	chr3:121444600-121455200	Weak transcription	Psoas Muscle	Psoas
5	chr3:121444600-121466400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:121444800-121457200	Weak transcription	Gastric	stomach
7	chr3:121444800-121457200	Weak transcription	Right Ventricle	heart
8	chr3:121444800-121457400	Weak transcription	Pancreas	Pancrea
9	chr3:121444800-121458800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:121444800-121458800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:121444800-121466400	Weak transcription	Colonic Mucosa	Colon
12	chr3:121444800-121467200	Weak transcription	Aorta	Aorta
13	chr3:121444800-121467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:121444800-121467400	Weak transcription	Spleen	Spleen
15	chr3:121445200-121457200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:121445200-121457800	Weak transcription	Lung	lung
17	chr3:121445200-121466200	Weak transcription	Fetal Intestine Small	intestine
18	chr3:121445200-121466800	Weak transcription	Thymus	Thymus
19	chr3:121445200-121467400	Weak transcription	Esophagus	oesophagus
20	chr3:121445800-121467000	Weak transcription	Fetal Stomach	stomach
21	chr3:121445800-121467400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:121446000-121451800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:121447400-121456800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:121447600-121467000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:121447800-121452400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:121447800-121466400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:121447800-121467000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:121448000-121453400	Weak transcription	A549	lung
29	chr3:121448000-121453800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:121448000-121457800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:121448000-121466400	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:121448000-121466400	Weak transcription	Fetal Kidney	kidney
33	chr3:121448200-121458400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:121448200-121458800	Weak transcription	Dnd41	blood
35	chr3:121448200-121466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:121448400-121452000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:121448400-121466400	Weak transcription	HSMM	muscle
38	chr3:121448400-121466800	Weak transcription	Hela-S3	cervix
39	chr3:121448600-121458800	Weak transcription	Adipose Nuclei	Adipose
40	chr3:121448600-121466400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:121448800-121452400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:121448800-121453000	Weak transcription	GM12878-XiMat	blood
43	chr3:121448800-121453400	Weak transcription	NHLF	lung
44	chr3:121448800-121453600	Weak transcription	NH-A	brain
45	chr3:121448800-121453600	Weak transcription	NHDF-Ad	bronchial
46	chr3:121448800-121453800	Weak transcription	Osteobl	bone
47	chr3:121448800-121455200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:121448800-121457400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:121448800-121457800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:121448800-121458800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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