Variant report

Variant	rs1938230
Chromosome Location	chr1:239609714-239609715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10157644	0.83[AMR][1000 genomes]
rs10754671	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10802771	0.86[AMR][1000 genomes]
rs10925884	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10925885	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10925888	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1796834	0.81[AMR][1000 genomes]
rs1796835	0.85[AMR][1000 genomes]
rs4263985	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4486441	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4557960	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4659545	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6429137	0.88[AMR][1000 genomes]
rs6429138	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6671410	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6685478	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6696246	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6699243	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7536688	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1006640	chr1:239290853-239658788	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535358	chr1:239290853-239658788	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873350	chr1:239498915-239648140	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239595400-239614200	Weak transcription	Pancreas	Pancrea
2	chr1:239597600-239613000	Weak transcription	Ovary	ovary
3	chr1:239608800-239612400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:239609000-239610000	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:239609600-239610000	Enhancers	Stomach Mucosa	stomach

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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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