Variant report

Variant	rs9625200
Chromosome Location	chr22:27700318-27700319
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:27644670..27647222-chr22:27697658..27700615,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11090481	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11090482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11912637	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165810	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165996	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170215	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13056368	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13056999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13058409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16984203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1997645	0.86[CHB][hapmap];0.90[YRI][hapmap]
rs516155	0.95[CEU][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57851794	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71325232	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71325233	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71325235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713818	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs736951	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs8135866	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[YRI][hapmap]
rs8137063	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap]
rs8137296	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8139966	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[YRI][hapmap]
rs8141513	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8142278	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9306439	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs9613422	0.87[ASN][1000 genomes]
rs9613424	0.86[CHB][hapmap]
rs9620680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9620683	0.87[ASN][1000 genomes]
rs9625199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv834166	chr22:27628570-27814359	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9625200	SEZ6L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27697000-27702600	Weak transcription	Fetal Brain Female	brain
2	chr22:27697000-27705800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:27698000-27702800	Weak transcription	Fetal Brain Male	brain
4	chr22:27698600-27706200	Weak transcription	Brain Germinal Matrix	brain

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