Variant report

Variant	rs1404999
Chromosome Location	chr7:39121465-39121466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10258862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273694	0.89[CHD][hapmap];0.83[MEX][hapmap]
rs1116813	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs11773650	0.95[ASN][1000 genomes]
rs12216590	1.00[CHD][hapmap]
rs12531458	0.89[CHB][hapmap];0.84[CHD][hapmap]
rs12531476	0.95[ASN][1000 genomes]
rs12531789	1.00[CHB][hapmap]
rs12540036	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs12701690	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs13234105	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs1358422	1.00[CHB][hapmap]
rs1527949	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs1534416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880005	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17171520	1.00[CHB][hapmap]
rs17171521	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs17171526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171527	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs1881132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35319478	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35787066	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs36065581	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1404999	S100G	trans	cerebellum	SCAN
rs1404999	KIAA0895	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39113600-39123400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:39115600-39125200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:39120400-39123600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:39121400-39123200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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