Variant report

Variant	rs197604
Chromosome Location	chr1:57679206-57679207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1053	0.89[TSI][hapmap]
rs155284	0.89[TSI][hapmap]
rs155286	0.92[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs197105	0.89[TSI][hapmap]
rs197597	0.92[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs197603	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197606	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs197607	0.92[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs197610	0.89[TSI][hapmap]
rs264036	0.83[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs2764660	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs490419	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs556131	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561248	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs619732	0.93[ASN][1000 genomes]
rs653386	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs197604	PODN	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57672400-57680600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:57672400-57680800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:57672600-57680800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:57675600-57692600	Weak transcription	Fetal Intestine Large	intestine
5	chr1:57675800-57680800	Weak transcription	Fetal Heart	heart
6	chr1:57676000-57689800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:57678600-57684600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:57678800-57680600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:57678800-57681000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:57679200-57695000	Weak transcription	Fetal Brain Female	brain

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

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