Variant report

Variant	rs2022003
Chromosome Location	chr1:158586966-158586967
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:158580471-158587575	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158584333..158587255-chr1:158593712..158595275,2	K562	blood:

Variant related genes	Relation type
SPTA1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11265005	0.82[CEU][hapmap]
rs16840314	0.82[CEU][hapmap]
rs2022002	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157691	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2246434	0.81[CEU][hapmap]
rs2251963	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251964	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2479861	0.87[CHB][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]
rs2479862	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2479868	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2482963	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518489	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518490	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518491	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2779116	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2852634	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2852635	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857684	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs857685	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs857688	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs857719	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs857720	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs857721	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs857725	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs860772	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs863327	0.81[MEX][hapmap]
rs863343	0.80[CEU][hapmap]
rs863344	0.82[CEU][hapmap]
rs863366	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs863368	0.87[CHB][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]

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	esv3491788	chr1:158537183-158725907	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3491789	chr1:158537242-158725858	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2022003	SCAMP3	cis	parietal	SCAN
rs2022003	PYHIN1	cis	cerebellum	SCAN
rs2022003	OR10Z1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158580200-158588800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:158581000-158598200	Strong transcription	K562	blood
3	chr1:158583600-158607600	Weak transcription	Primary B cells from cord blood	blood

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