Variant report

Variant	rs1053
Chromosome Location	chr1:57671663-57671664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs155284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs155285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs197101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197103	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs197105	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs197597	0.87[TSI][hapmap]
rs197598	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs197600	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs197602	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs197604	0.89[TSI][hapmap]
rs197605	0.89[TSI][hapmap]
rs197610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264037	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264038	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502350	0.82[CEU][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	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
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1053	HOOK1	cis	parietal	SCAN
rs1053	SLC1A7	cis	cerebellum	SCAN
rs1053	PODN	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57664600-57678400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:57669800-57672400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:57670200-57672400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
4	chr1:57670200-57672400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57670200-57672400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr1:57670200-57672400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr1:57670200-57672400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:57670400-57672400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:57670400-57672400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:57670400-57672600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:57670600-57672400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:57670600-57672600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:57670800-57672400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:57670800-57672400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:57670800-57672600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:57671000-57673800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:57671000-57674600	Weak transcription	Fetal Brain Female	brain
18	chr1:57671200-57672400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
19	chr1:57671200-57673600	Weak transcription	Fetal Intestine Large	intestine
20	chr1:57671600-57671800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr1:57671600-57672200	Enhancers	Fetal Brain Male	brain
22	chr1:57671600-57672400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr1:57671600-57672400	Enhancers	Fetal Heart	heart
24	chr1:57671600-57672600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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