Variant report

Variant	rs62139780
Chromosome Location	chr2:53893386-53893387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10865275	0.82[AFR][1000 genomes]
rs11125515	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682721	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11684084	0.88[ASN][1000 genomes]
rs11889094	0.98[ASN][1000 genomes]
rs11902691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12611475	0.92[ASN][1000 genomes]
rs12620583	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2080715	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2111852	0.82[AMR][1000 genomes]
rs2160929	0.95[ASN][1000 genomes]
rs2193682	0.88[ASN][1000 genomes]
rs2193683	0.88[ASN][1000 genomes]
rs3770403	0.85[ASN][1000 genomes]
rs3770405	0.84[ASN][1000 genomes]
rs56081372	0.90[ASN][1000 genomes]
rs56291505	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62139772	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62139783	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62139835	0.94[ASN][1000 genomes]
rs6705712	0.80[ASN][1000 genomes]
rs6713107	0.97[ASN][1000 genomes]
rs6714891	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727876	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6728355	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6741239	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6743627	0.92[ASN][1000 genomes]
rs6757393	0.92[ASN][1000 genomes]
rs7556791	0.97[ASN][1000 genomes]
rs7557799	0.94[ASN][1000 genomes]
rs7557898	0.94[ASN][1000 genomes]
rs7563054	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7584474	0.94[ASN][1000 genomes]
rs7587217	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53879400-53895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:53881200-53895800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:53881800-53896400	Weak transcription	Aorta	Aorta
6	chr2:53882600-53894000	Weak transcription	Fetal Stomach	stomach
7	chr2:53882800-53895600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:53883200-53897800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:53883600-53896600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:53885000-53895800	Weak transcription	Dnd41	blood
11	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
12	chr2:53885800-53911800	Weak transcription	Adipose Nuclei	Adipose
13	chr2:53886600-53896400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:53887000-53895400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:53887000-53898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:53887800-53899800	Weak transcription	Primary B cells from cord blood	blood
17	chr2:53888200-53934200	Weak transcription	Lung	lung
18	chr2:53888400-53896000	Weak transcription	Primary T cells from cord blood	blood
19	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
20	chr2:53888600-53897200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
22	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:53889400-53895800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:53889400-53896800	Weak transcription	Fetal Lung	lung
25	chr2:53889800-53895800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:53891600-53900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:53892600-53902600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:53892600-53918800	Weak transcription	Left Ventricle	heart

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