Variant report

Variant	rs689342
Chromosome Location	chr1:57485242-57485243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1342435	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411013	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1411014	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418473	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418475	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17409911	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1774888	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1774905	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1774910	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251154	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs515493	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526259	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs630417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs661586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72641113	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs947655	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57474200-57490200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:57477600-57490200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:57479400-57487000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:57481600-57490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:57483200-57494000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:57483400-57490400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:57483400-57490600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:57483600-57490600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:57484400-57485400	Enhancers	Liver	Liver
10	chr1:57484400-57485400	Enhancers	HepG2	liver
11	chr1:57484400-57485600	Genic enhancers	Fetal Intestine Small	intestine
12	chr1:57484400-57486000	Enhancers	Fetal Brain Male	brain
13	chr1:57484600-57485400	Enhancers	Brain Germinal Matrix	brain
14	chr1:57484800-57485400	Enhancers	Duodenum Mucosa	Duodenum
15	chr1:57485000-57486000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:57485200-57494800	Weak transcription	Fetal Brain Female	brain

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

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