Variant report

Variant	rs828842
Chromosome Location	chr2:74355244-74355245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1667613	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667614	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667618	0.84[CEU][hapmap]
rs1723289	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3099824	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4271791	0.85[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6715731	0.84[EUR][1000 genomes]
rs828844	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828866	0.82[EUR][1000 genomes]
rs828879	0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[ASN][1000 genomes]
rs828881	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs828899	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs828900	0.93[EUR][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	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs828842	FNBP1P1	cis	Esophagus Mucosa	GTEx
rs828842	MGC10955	cis	Thyroid	GTEx
rs828842	FNBP1P1	cis	Muscle Skeletal	GTEx
rs828842	FNBP1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs828842	NAT8	cis	parietal	SCAN
rs828842	DQX1	cis	parietal	SCAN
rs828842	FNBP1P1	cis	Esophagus Muscularis	GTEx
rs828842	FNBP1P1	cis	Nerve Tibial	GTEx
rs828842	FAM136A	cis	cerebellum	SCAN
rs828842	FNBP1P1	cis	Thyroid	GTEx
rs828842	FNBP1P1	cis	Adipose Subcutaneous	GTEx
rs828842	FNBP1P1	cis	Artery Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74348000-74357400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:74348200-74360400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:74348200-74367600	Weak transcription	Brain Anterior Caudate	brain
4	chr2:74348600-74361800	Weak transcription	Hela-S3	cervix
5	chr2:74348800-74360400	Weak transcription	Primary T cells from cord blood	blood
6	chr2:74350800-74360400	Weak transcription	Brain Substantia Nigra	brain
7	chr2:74351200-74358400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:74353400-74360400	Weak transcription	Dnd41	blood
9	chr2:74353600-74360400	Weak transcription	A549	lung
10	chr2:74354200-74359400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:74354400-74373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:74354800-74360400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:74355200-74373800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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