Variant report

Variant	rs66684820
Chromosome Location	chr2:53880040-53880041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10185375	0.82[EUR][1000 genomes]
rs10210726	0.93[EUR][1000 genomes]
rs12612737	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12612895	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12613682	0.93[EUR][1000 genomes]
rs12614610	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616124	0.87[EUR][1000 genomes]
rs12617315	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617360	0.82[EUR][1000 genomes]
rs12617668	0.89[EUR][1000 genomes]
rs12618833	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12621557	0.87[EUR][1000 genomes]
rs12621635	0.87[EUR][1000 genomes]
rs13415842	0.85[EUR][1000 genomes]
rs13421512	0.84[EUR][1000 genomes]
rs17045114	0.83[ASN][1000 genomes]
rs17045116	0.83[ASN][1000 genomes]
rs17045125	0.91[EUR][1000 genomes]
rs17045215	0.82[EUR][1000 genomes]
rs2009149	0.93[EUR][1000 genomes]
rs2058953	0.95[ASN][1000 genomes]
rs2287344	0.82[EUR][1000 genomes]
rs2287512	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2357491	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2357492	0.92[ASN][1000 genomes]
rs35833242	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770401	0.87[EUR][1000 genomes]
rs3770410	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770412	0.89[ASN][1000 genomes]
rs3770415	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4361164	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56189833	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67073722	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6716301	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6760101	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68123661	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7595713	0.89[EUR][1000 genomes]
rs991599	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs994484	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997644	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv874147	chr2:53772561-53886799	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53878800-53880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:53879200-53880400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:53879400-53880200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:53879400-53895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:53879600-53880800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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