Variant report

Variant	rs999218
Chromosome Location	chr2:178567474-178567475
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178557827..178560384-chr2:178566181..178567818,2	K562	blood:
2	chr2:178561612..178563811-chr2:178565917..178568583,4	K562	blood:
3	chr2:178561119..178564111-chr2:178566483..178568629,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AGPS-3	chr2:178567216-178567477	ENSG00000229941.1
2	lnc-AGPS-3	chr2:178567216-178567477	ENSG00000229941.1

Variant related genes	Relation type
ENSG00000229941	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1004541	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004542	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192481	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201180	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930805	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677821	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12987101	0.85[EUR][1000 genomes]
rs12989020	0.85[EUR][1000 genomes]
rs13012431	0.85[EUR][1000 genomes]
rs13428806	0.80[AMR][1000 genomes]
rs1344917	0.85[AMR][1000 genomes]
rs1347731	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370662	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370664	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438037	0.82[AMR][1000 genomes]
rs1438038	0.85[AMR][1000 genomes]
rs1438039	0.82[AMR][1000 genomes]
rs1438054	0.88[ASN][1000 genomes]
rs1438055	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1469972	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469973	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561315	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1561319	0.85[AMR][1000 genomes]
rs16865726	0.85[AMR][1000 genomes]
rs17400512	0.85[EUR][1000 genomes]
rs1866210	0.80[AMR][1000 genomes]
rs1866211	0.82[AMR][1000 genomes]
rs1866212	0.82[AMR][1000 genomes]
rs1975321	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975323	0.80[AMR][1000 genomes]
rs1975324	0.82[AMR][1000 genomes]
rs2033760	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164857	0.85[AMR][1000 genomes]
rs2164860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365889	0.82[AMR][1000 genomes]
rs2886424	0.90[ASN][1000 genomes]
rs2886498	0.82[AMR][1000 genomes]
rs3731809	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754993	0.85[AMR][1000 genomes]
rs3754994	0.82[AMR][1000 genomes]
rs3770023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770034	0.82[AMR][1000 genomes]
rs3770042	0.80[AMR][1000 genomes]
rs4893980	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4893981	0.88[ASN][1000 genomes]
rs4893982	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4893984	0.88[ASN][1000 genomes]
rs4893985	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433693	0.82[AMR][1000 genomes]
rs6718702	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760930	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749208	0.85[AMR][1000 genomes]
rs7596360	0.88[ASN][1000 genomes]
rs934809	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998061	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
3	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv870023	chr2:178545623-178581407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1005854	chr2:178546907-178586608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2762967	chr2:178546919-178577002	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1005991	chr2:178550049-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1003983	chr2:178551958-178577002	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178558200-178576600	Weak transcription	Pancreas	Pancrea
2	chr2:178563000-178574800	Weak transcription	Fetal Muscle Leg	muscle

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