Variant report

Variant	rs9430001
Chromosome Location	chr1:209769109-209769110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10489338	1.00[CHB][hapmap]
rs11119309	1.00[CHB][hapmap]
rs12058586	1.00[CHB][hapmap]
rs12119742	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014825	0.85[CHB][hapmap]
rs17014842	0.85[CHB][hapmap]
rs2072908	0.83[CHB][hapmap]
rs2076225	0.86[CHB][hapmap]
rs2076229	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6690557	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7512091	0.80[CHB][hapmap]
rs7528698	0.82[YRI][hapmap]
rs9429820	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429821	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9430000	1.00[CHB][hapmap]
rs9430002	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9430003	0.94[EUR][1000 genomes];0.98[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9430001	RP1-272L16.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209760600-209776400	Weak transcription	Fetal Lung	lung
2	chr1:209764200-209776600	Weak transcription	Ovary	ovary
3	chr1:209764200-209780400	Weak transcription	Fetal Brain Male	brain
4	chr1:209764600-209791200	Weak transcription	Brain Anterior Caudate	brain
5	chr1:209765400-209776800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:209768000-209773800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:209768400-209769800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:209768800-209769600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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Input of quick search could be:

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

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