Variant report

Variant	rs57273516
Chromosome Location	chr3:49483074-49483075
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	chr3:49376057..49377754-chr3:49482622..49485601,2	K562	blood:

Variant related genes	Relation type
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1009051	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10155014	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	0.88[EUR][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11130187	0.81[AMR][1000 genomes]
rs11130190	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11710434	0.81[AMR][1000 genomes]
rs11715060	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11719762	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720542	0.81[AMR][1000 genomes]
rs11720657	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11923032	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11928090	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	0.89[EUR][1000 genomes]
rs13096474	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.91[EUR][1000 genomes]
rs1464569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2177268	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2312462	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329025	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3866330	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855837	0.85[EUR][1000 genomes]
rs4855853	0.87[EUR][1000 genomes]
rs4855858	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4955413	0.81[EUR][1000 genomes]
rs4955417	1.00[ASN][1000 genomes]
rs4955424	0.82[EUR][1000 genomes]
rs4955425	0.81[EUR][1000 genomes]
rs4955430	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56127630	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62259933	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62259943	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62259944	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62259947	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62261183	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62261249	0.89[EUR][1000 genomes]
rs6446262	0.84[EUR][1000 genomes]
rs6446275	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6769744	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775069	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6783003	0.93[EUR][1000 genomes]
rs6784203	0.82[EUR][1000 genomes]
rs6785045	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6796147	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6805609	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6809204	0.82[EUR][1000 genomes]
rs72934271	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73073004	0.82[EUR][1000 genomes]
rs73088137	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7355800	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7374731	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7613491	0.94[EUR][1000 genomes]
rs7619789	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7625857	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7638750	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7644148	0.90[EUR][1000 genomes]
rs7647973	0.94[EUR][1000 genomes]
rs7648995	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7651372	0.91[EUR][1000 genomes]
rs7653505	0.86[AFR][1000 genomes]
rs8897	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs940045	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs974495	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757181	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9809237	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9817807	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9842132	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9860055	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9861027	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9862534	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs57273516	NICN1	cis	Thyroid	GTEx
rs57273516	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs57273516	WDR6	cis	lung	GTEx
rs57273516	WDR6	cis	Esophagus Muscularis	GTEx
rs57273516	AMT	cis	Adipose Subcutaneous	GTEx
rs57273516	NICN1-AS1	cis	Thyroid	GTEx
rs57273516	AMT	cis	Whole Blood	GTEx
rs57273516	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs57273516	AMT	cis	Esophagus Mucosa	GTEx
rs57273516	AMT	cis	Artery Aorta	GTEx
rs57273516	AMT	cis	Thyroid	GTEx
rs57273516	AMT	cis	lung	GTEx
rs57273516	AMT	cis	Artery Tibial	GTEx
rs57273516	WDR6	cis	Nerve Tibial	GTEx
rs57273516	AMT	cis	Muscle Skeletal	GTEx
rs57273516	AMT	cis	Esophagus Muscularis	GTEx
rs57273516	WDR6	cis	Muscle Skeletal	GTEx
rs57273516	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs57273516	AMT	cis	Nerve Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49467400-49486400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49480000-49484200	Enhancers	Placenta	Placenta
3	chr3:49480400-49484400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:49480400-49484400	Enhancers	Primary B cells from cord blood	blood
5	chr3:49481200-49483200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr3:49481600-49483200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:49481600-49484200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:49481600-49486400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:49481600-49486400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:49481600-49486400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:49481600-49486400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:49481600-49486400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:49481600-49486400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:49481600-49486400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:49481600-49486400	Weak transcription	HUVEC	blood vessel
16	chr3:49481600-49486400	Weak transcription	NHDF-Ad	bronchial
17	chr3:49481600-49486400	Weak transcription	NHEK	skin
18	chr3:49481800-49484000	Weak transcription	Hela-S3	cervix
19	chr3:49481800-49486400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:49481800-49486400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:49481800-49486400	Weak transcription	K562	blood
22	chr3:49481800-49486400	Weak transcription	Osteobl	bone
23	chr3:49481800-49492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:49482000-49486400	Weak transcription	Adipose Nuclei	Adipose
25	chr3:49482000-49486400	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:49482000-49498200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:49482200-49486400	Weak transcription	Thymus	Thymus
28	chr3:49482400-49486400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:49482400-49486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:49482400-49486400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:49482400-49486400	Weak transcription	Fetal Thymus	thymus
32	chr3:49482400-49486400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:49482600-49486200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:49482600-49486400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:49482600-49486400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:49482600-49486400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:49482600-49486400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:49482600-49486400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:49482600-49486400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:49482600-49486400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:49482600-49486400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:49482600-49486400	Weak transcription	GM12878-XiMat	blood
43	chr3:49482800-49486400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:49483000-49483200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:49483000-49486400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:49483000-49486400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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