Variant report

Variant	rs269042
Chromosome Location	chr1:57874048-57874049
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10047072	0.83[EUR][1000 genomes]
rs10047179	0.83[EUR][1000 genomes]
rs10493221	0.90[JPT][hapmap]
rs10889037	0.82[CHB][hapmap]
rs10889038	0.90[JPT][hapmap];0.82[TSI][hapmap]
rs10889039	0.90[JPT][hapmap];0.82[TSI][hapmap]
rs10889041	0.83[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs10889042	0.90[JPT][hapmap]
rs11207026	0.90[JPT][hapmap]
rs11207027	0.88[JPT][hapmap]
rs12067263	0.83[EUR][1000 genomes]
rs1240442	0.83[EUR][1000 genomes]
rs1240443	0.83[EUR][1000 genomes]
rs1424463	0.86[JPT][hapmap]
rs1424465	0.81[GIH][hapmap]
rs1424467	0.80[TSI][hapmap]
rs1557222	0.83[EUR][1000 genomes]
rs17115750	0.90[JPT][hapmap]
rs17423255	0.80[TSI][hapmap]
rs17458730	0.90[JPT][hapmap]
rs1778032	0.90[JPT][hapmap]
rs1862925	0.81[GIH][hapmap];0.82[MEX][hapmap]
rs2113453	0.81[EUR][1000 genomes]
rs2405697	0.81[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs269038	0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs269039	0.83[EUR][1000 genomes]
rs269044	0.90[JPT][hapmap]
rs269045	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs269048	0.90[JPT][hapmap]
rs269049	0.90[JPT][hapmap]
rs269050	0.90[JPT][hapmap]
rs269051	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs269057	0.89[JPT][hapmap]
rs3738553	0.90[JPT][hapmap]
rs3844041	0.90[JPT][hapmap]
rs3850549	0.90[JPT][hapmap]
rs3850550	0.90[JPT][hapmap]
rs3850552	0.90[JPT][hapmap]
rs3861833	0.81[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs3861834	0.90[JPT][hapmap]
rs3896279	0.90[JPT][hapmap]
rs3909558	0.83[EUR][1000 genomes]
rs499339	0.81[CHB][hapmap]
rs532926	0.90[JPT][hapmap]
rs540431	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs563099	0.90[JPT][hapmap]
rs563270	0.90[JPT][hapmap];0.82[MEX][hapmap]
rs565032	0.86[JPT][hapmap]
rs566847	0.90[JPT][hapmap]
rs567773	0.92[CEU][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs574726	0.81[CHB][hapmap]
rs6687934	0.81[GIH][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs269042	DAB1	cis	cerebellum	SCAN
rs269042	MRPL37	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57860400-57874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:57863800-57875400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:57867600-57874400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:57867800-57874600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:57867800-57875400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:57870400-57874800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:57870400-57874800	Enhancers	Fetal Brain Male	brain
8	chr1:57871000-57887600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:57873000-57874400	Enhancers	Fetal Brain Female	brain
10	chr1:57873000-57874600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:57873000-57874600	Enhancers	Stomach Smooth Muscle	stomach
12	chr1:57873200-57875000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:57873200-57877200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:57873400-57874600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:57873600-57874200	Enhancers	Stomach Mucosa	stomach
16	chr1:57873600-57874200	Enhancers	HepG2	liver
17	chr1:57873600-57874600	Enhancers	Colon Smooth Muscle	Colon
18	chr1:57873600-57874800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:57873600-57877600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:57873800-57874600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:57873800-57874600	Enhancers	Fetal Stomach	stomach
22	chr1:57873800-57875000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:57874000-57874200	Enhancers	Fetal Heart	heart
24	chr1:57874000-57874400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr1:57874000-57874800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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