Variant report

Variant	rs4233435
Chromosome Location	chr1:90738800-90738801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10754300	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10801800	0.87[ASN][1000 genomes]
rs10922815	0.81[ASN][1000 genomes]
rs10922818	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10922819	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12021593	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12046150	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12058249	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12060187	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12733919	0.90[ASN][1000 genomes]
rs3923534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128959	0.93[ASN][1000 genomes]
rs4233434	0.82[ASN][1000 genomes]
rs4417049	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4418580	0.98[ASN][1000 genomes]
rs4440840	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4507991	0.89[ASN][1000 genomes]
rs4535988	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4623679	0.96[ASN][1000 genomes]
rs4658150	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6428584	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6679092	0.95[ASN][1000 genomes]
rs6689390	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689724	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6690274	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694176	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531149	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7548218	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9651073	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv546803	chr1:90679734-90777717	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv524317	chr1:90729744-90836739	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4233435	FAM69A	cis	cerebellum	SCAN
rs4233435	ZNF326	cis	cerebellum	SCAN
rs4233435	LRRC8B	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:90736200-90752000	Weak transcription	Aorta	Aorta
2	chr1:90737800-90738800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:90738400-90739800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:90738400-90740200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:90738800-90739200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:90738800-90739800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:90738800-90740200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:90738800-90741200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr1:90738800-90741600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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