Variant report

Variant	rs17679952
Chromosome Location	chr2:7388387-7388388
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10205823	0.85[ASN][1000 genomes]
rs17628484	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17629193	0.81[ASN][1000 genomes]
rs17629326	0.85[ASN][1000 genomes]
rs17678724	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17679999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2056635	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2056637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2059984	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4668533	0.85[ASN][1000 genomes]
rs55751069	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55900254	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58433699	0.85[ASN][1000 genomes]
rs62104707	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs62104708	0.90[ASN][1000 genomes]
rs62104709	0.90[ASN][1000 genomes]
rs62104710	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6720017	0.85[ASN][1000 genomes]
rs6724621	0.85[ASN][1000 genomes]
rs72770038	0.90[ASN][1000 genomes]
rs72770045	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72770048	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72770050	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72770051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72770052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72770055	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72770056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72770057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72770059	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72770065	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7556844	0.81[ASN][1000 genomes]
rs7599240	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915888	chr2:7197783-7461967	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv833337	chr2:7337273-7521146	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17679952	HPCAL1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7372000-7388400	Weak transcription	Pancreas	Pancrea
2	chr2:7378000-7388400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:7383200-7399800	Weak transcription	Spleen	Spleen
4	chr2:7386400-7389400	Weak transcription	Fetal Brain Male	brain

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