Variant report

Variant	rs41281477
Chromosome Location	chr2:48847868-48847869
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48837425..48839347-chr2:48846973..48850503,3	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10198501	0.97[ASN][1000 genomes]
rs10208754	0.88[ASN][1000 genomes]
rs10209208	0.91[ASN][1000 genomes]
rs10495955	1.00[ASN][1000 genomes]
rs11125178	0.82[ASN][1000 genomes]
rs11676166	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11677854	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11678398	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11679449	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683643	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685904	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689544	0.82[AMR][1000 genomes]
rs11691408	0.84[ASN][1000 genomes]
rs11694191	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11901588	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12329215	0.91[ASN][1000 genomes]
rs12473064	0.91[ASN][1000 genomes]
rs12987384	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987494	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992138	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992918	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993815	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995714	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12997569	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014919	0.87[ASN][1000 genomes]
rs13022553	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13022734	1.00[ASN][1000 genomes]
rs13024367	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1404051	0.84[ASN][1000 genomes]
rs1404054	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524155	0.97[ASN][1000 genomes]
rs1589749	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17326209	0.84[ASN][1000 genomes]
rs17398030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916838	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1996969	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2056581	0.85[ASN][1000 genomes]
rs2103113	0.97[ASN][1000 genomes]
rs2293269	0.94[ASN][1000 genomes]
rs2349099	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34002966	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34003293	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34124947	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34205206	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34378457	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34393991	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34757099	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34790224	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35125065	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35362799	1.00[ASN][1000 genomes]
rs35422158	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35461667	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35501278	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35540486	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35737133	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35866214	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3792240	1.00[ASN][1000 genomes]
rs3792241	0.97[ASN][1000 genomes]
rs3792242	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792243	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429518	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62137487	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62137505	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62137532	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6545054	0.97[ASN][1000 genomes]
rs6706586	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6710333	1.00[ASN][1000 genomes]
rs6720650	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6723170	0.97[ASN][1000 genomes]
rs6730379	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6734199	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6738387	1.00[ASN][1000 genomes]
rs6739692	1.00[ASN][1000 genomes]
rs6741840	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6746623	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6747475	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6747688	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6749600	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6760849	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7559006	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7562038	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7572902	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7587112	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7601997	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active 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
11	nsv874004	chr2:48838955-48904550	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2762553	chr2:48843520-48863842	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv2719	chr2:48847455-48867113	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41281477	STON1-GTF2A1L	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48831000-48859600	Weak transcription	Ovary	ovary
2	chr2:48836600-48862000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:48847000-48853000	Weak transcription	Colon Smooth Muscle	Colon

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