Variant report

Variant	rs947239
Chromosome Location	chr1:57999135-57999136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11589538	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1357785	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357786	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1357787	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1404390	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1524727	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1608691	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2691439	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793627	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2793631	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793632	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793633	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2805846	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2805847	1.00[CEU][hapmap];0.84[YRI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2805848	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2805884	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4912255	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72676943	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv870908	chr1:57884310-58037783	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv870802	chr1:57965114-58037031	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57988600-58001400	Weak transcription	Stomach Mucosa	stomach
2	chr1:57989200-58012200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57997600-57999800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:57998400-58000000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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