Variant report

Variant	rs857725
Chromosome Location	chr1:158607935-158607936
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158604204..158606643-chr1:158606798..158609046,2	K562	blood:
2	chr1:158586569..158589083-chr1:158607491..158610160,2	K562	blood:

Variant related genes	Relation type
ENSG00000163554	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1029083	0.83[EUR][1000 genomes]
rs16840314	0.86[CEU][hapmap]
rs2022002	0.80[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2022003	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]
rs2157691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246434	0.86[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.87[EUR][1000 genomes]
rs2251963	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251964	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2479861	0.87[CHB][hapmap]
rs2479862	0.87[CHB][hapmap]
rs2479868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2482963	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2518489	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518490	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518491	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518493	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2779116	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2852634	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2852635	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2852637	0.83[EUR][1000 genomes]
rs857684	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs857685	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs857688	0.87[CHB][hapmap]
rs857689	0.85[EUR][1000 genomes]
rs857691	0.80[EUR][1000 genomes]
rs857719	0.87[CHB][hapmap]
rs857720	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857721	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs860772	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs861409	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs863327	0.81[CEU][hapmap];0.90[MEX][hapmap];0.85[EUR][1000 genomes]
rs863343	0.85[CEU][hapmap]
rs863344	0.86[CEU][hapmap]
rs863366	0.87[CHB][hapmap]
rs863368	0.87[CHB][hapmap]
rs950488	0.81[CEU][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs857725	PYHIN1	cis	cerebellum	SCAN
rs857725	SCAMP3	cis	parietal	SCAN
rs857725	SLC27A3	cis	cerebellum	SCAN
rs857725	OR10Z1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158603800-158610200	Strong transcription	K562	blood
2	chr1:158607400-158608600	Strong transcription	Primary hematopoietic stem cells	blood
3	chr1:158607600-158608400	Strong transcription	Primary B cells from cord blood	blood
4	chr1:158607800-158609800	Enhancers	Fetal Lung	lung

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