Variant report

Variant	rs56819945
Chromosome Location	chr2:85755139-85755140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85752002..85755220-chr2:85755713..85758513,4	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11126995	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11895341	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895399	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895401	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615553	0.84[ASN][1000 genomes]
rs13394343	0.81[ASN][1000 genomes]
rs1446669	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026396	0.81[ASN][1000 genomes]
rs2028898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2043675	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2044474	0.81[ASN][1000 genomes]
rs2289972	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592551	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731828	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755008	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55692129	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58307667	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58644336	0.90[ASN][1000 genomes]
rs58768785	0.84[ASN][1000 genomes]
rs59877521	0.81[ASN][1000 genomes]
rs60012532	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60788310	0.83[ASN][1000 genomes]
rs6547620	0.81[ASN][1000 genomes]
rs6547622	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6714709	0.81[ASN][1000 genomes]
rs6721924	0.82[ASN][1000 genomes]
rs6722691	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6733913	0.81[ASN][1000 genomes]
rs6735663	0.91[ASN][1000 genomes]
rs6739015	0.81[ASN][1000 genomes]
rs6743030	0.81[ASN][1000 genomes]
rs6750847	0.81[ASN][1000 genomes]
rs67988001	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs699664	0.98[ASN][1000 genomes]
rs72643495	0.92[ASN][1000 genomes]
rs73943244	0.83[ASN][1000 genomes]
rs7579147	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7593969	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7608074	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs762684	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56819945	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs56819945	VAMP8	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85734600-85762000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:85745000-85764800	Weak transcription	Esophagus	oesophagus
3	chr2:85751200-85764000	Weak transcription	Psoas Muscle	Psoas
4	chr2:85751200-85764400	Weak transcription	Small Intestine	intestine
5	chr2:85752000-85764800	Weak transcription	Gastric	stomach
6	chr2:85752400-85764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:85752600-85758200	Weak transcription	Pancreas	Pancrea
8	chr2:85752600-85763600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:85752800-85758200	Weak transcription	Brain Angular Gyrus	brain
10	chr2:85752800-85758200	Weak transcription	Brain Anterior Caudate	brain
11	chr2:85752800-85761600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:85753000-85758200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:85753000-85758200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:85753000-85758400	Weak transcription	Stomach Mucosa	stomach
15	chr2:85753000-85764000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:85753200-85758200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:85753200-85761000	Weak transcription	Primary B cells from cord blood	blood
18	chr2:85754600-85756000	Enhancers	Liver	Liver
19	chr2:85754800-85755400	Enhancers	Pancreatic Islets	Pancreatic Islet

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