Variant report

Variant	rs4657470
Chromosome Location	chr1:165686763-165686764
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10800150	0.81[CHD][hapmap]
rs10800152	0.86[CHB][hapmap]
rs10918266	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10918276	0.87[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10918281	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs12021678	0.81[CHD][hapmap]
rs12028087	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12723198	0.88[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs14223	0.88[CEU][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1913846	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2814470	0.88[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs4656461	0.81[YRI][hapmap]
rs4656462	0.86[CHB][hapmap]
rs6426937	0.88[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6426940	0.88[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs6670705	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7411708	0.88[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs7512095	0.86[EUR][1000 genomes]
rs7540840	0.83[EUR][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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4657470	IGSF8	cis	cerebellum	SCAN
rs4657470	FCGR3A	cis	parietal	SCAN
rs4657470	SH2D1B	cis	parietal	SCAN
rs4657470	ADCY10	cis	parietal	SCAN
rs4657470	UAP1	cis	cerebellum	SCAN
rs4657470	ARHGAP30	cis	parietal	SCAN
rs4657470	GMIP	trans	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165684400-165687600	Enhancers	Liver	Liver
2	chr1:165685200-165687600	Enhancers	HepG2	liver
3	chr1:165685200-165695400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:165685200-165696600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:165685200-165721600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:165685400-165687400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:165685600-165705200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:165686400-165687000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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