Variant report

Variant	rs62261249
Chromosome Location	chr3:49594060-49594061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr3:49593948-49594231	K562	blood:	n/a	chr3:49594125-49594134 chr3:49594118-49594139
2	TEAD4	chr3:49593901-49594307	K562	blood:	n/a	n/a
3	STAT5A	chr3:49593938-49594313	K562	blood:	n/a	n/a
4	EP300	chr3:49593956-49594252	K562	blood:	n/a	n/a
5	TAL1	chr3:49593941-49594289	K562	blood:	n/a	chr3:49594073-49594082
6	TEAD4	chr3:49593944-49594319	K562	blood:	n/a	n/a
7	SPI1	chr3:49594030-49594235	K562	blood:	n/a	chr3:49594159-49594166 chr3:49594156-49594169
8	MEF2A	chr3:49593946-49594371	K562	blood:	n/a	chr3:49594190-49594205
9	RCOR1	chr3:49593924-49594328	K562	blood:	n/a	n/a
10	GATA2	chr3:49594005-49594260	K562	blood:	n/a	chr3:49594125-49594134 chr3:49594118-49594139
11	SPI1	chr3:49594057-49594272	K562	blood:	n/a	chr3:49594159-49594166 chr3:49594156-49594169
12	YY1	chr3:49594039-49594164	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49377286..49379479-chr3:49593352..49595591,2	K562	blood:
2	chr3:49593547..49595317-chr3:49595809..49597348,2	K562	blood:
3	chr3:49593038..49595710-chr3:49724290..49725804,2	MCF-7	breast:

Variant related genes	Relation type
BSN-AS2	TF binding region
ENSG00000173531	Chromatin interaction
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1009051	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10155014	0.82[EUR][1000 genomes]
rs10452032	1.00[ASN][1000 genomes]
rs1078341	1.00[ASN][1000 genomes]
rs10865956	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.88[EUR][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130204	0.85[EUR][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11130217	1.00[ASN][1000 genomes]
rs11709734	1.00[ASN][1000 genomes]
rs11710434	1.00[ASN][1000 genomes]
rs11720542	1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	1.00[ASN][1000 genomes]
rs11928090	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12583	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13096474	0.82[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.85[EUR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2029591	1.00[ASN][1000 genomes]
rs2131108	1.00[ASN][1000 genomes]
rs2140270	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.89[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs3866330	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3870339	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3870341	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3905330	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4052546	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4241407	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855837	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855845	1.00[ASN][1000 genomes]
rs4855846	1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855858	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4855869	0.85[EUR][1000 genomes]
rs4855885	1.00[ASN][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs56049603	0.83[EUR][1000 genomes]
rs56127630	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56324858	0.81[EUR][1000 genomes]
rs57273516	0.89[EUR][1000 genomes]
rs62259933	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446275	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6778080	1.00[ASN][1000 genomes]
rs6783003	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6785045	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs72934271	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.92[EUR][1000 genomes]
rs7613491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619789	0.89[EUR][1000 genomes]
rs7620024	0.83[EUR][1000 genomes]
rs7622786	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7625857	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7647973	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.84[EUR][1000 genomes]
rs9654010	0.84[EUR][1000 genomes]
rs9809237	0.89[EUR][1000 genomes]
rs9817807	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9842132	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9871024	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	1.00[ASN][1000 genomes]
rs9883000	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs62261249	AMT	cis	Esophagus Mucosa	GTEx
rs62261249	AMT	cis	Muscle Skeletal	GTEx
rs62261249	AMT	cis	lung	GTEx
rs62261249	ARIH2	cis	Thyroid	GTEx
rs62261249	NICN1-AS1	cis	Thyroid	GTEx
rs62261249	WDR6	cis	Muscle Skeletal	GTEx
rs62261249	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs62261249	AMT	cis	Adipose Subcutaneous	GTEx
rs62261249	AMT	cis	Whole Blood	GTEx
rs62261249	RHOA	cis	Muscle Skeletal	GTEx
rs62261249	WDR6	cis	Nerve Tibial	GTEx
rs62261249	AMT	cis	Esophagus Muscularis	GTEx
rs62261249	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs62261249	AMT	cis	Stomach	GTEx
rs62261249	AMT	cis	Artery Aorta	GTEx
rs62261249	AMT	cis	Artery Tibial	GTEx
rs62261249	NICN1	cis	Thyroid	GTEx
rs62261249	AMT	cis	Nerve Tibial	GTEx
rs62261249	AMT	cis	Thyroid	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49591400-49594400	Active TSS	Brain Anterior Caudate	brain
2	chr3:49591600-49594400	Active TSS	Brain Angular Gyrus	brain
3	chr3:49592800-49594600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:49592800-49594800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:49592800-49596400	Weak transcription	Lung	lung
6	chr3:49593000-49596800	Weak transcription	Dnd41	blood
7	chr3:49593200-49595600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:49593400-49594600	Enhancers	Fetal Brain Male	brain
9	chr3:49593600-49594200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:49593600-49594400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
11	chr3:49593600-49594600	Enhancers	K562	blood
12	chr3:49593600-49595400	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:49593600-49595600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:49593800-49594600	Genic enhancers	Brain Germinal Matrix	brain
15	chr3:49594000-49595400	Weak transcription	Brain Cingulate Gyrus	brain

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