Variant report

Variant	rs197105
Chromosome Location	chr1:57677319-57677320
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1053	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]
rs155284	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs155285	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs197101	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs197103	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs197597	0.87[TSI][hapmap]
rs197598	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs197600	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs197601	0.85[AMR][1000 genomes]
rs197602	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs197604	0.89[TSI][hapmap]
rs197605	0.89[TSI][hapmap]
rs197610	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs264037	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs264038	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs502350	0.82[CEU][hapmap]
rs606497	0.81[LWK][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
rs197105	HOOK1	cis	parietal	SCAN
rs197105	C1orf177	cis	parietal	SCAN
rs197105	PODN	cis	parietal	SCAN

Chromatin state (count:9 , 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	chr1:57672400-57680600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:57672400-57680800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:57672600-57680800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:57675600-57678600	Weak transcription	Fetal Brain Male	brain
6	chr1:57675600-57678600	Weak transcription	Fetal Brain Female	brain
7	chr1:57675600-57692600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:57675800-57680800	Weak transcription	Fetal Heart	heart
9	chr1:57676000-57689800	Weak transcription	Fetal Intestine Small	intestine

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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