Variant report

Variant	rs857684
Chromosome Location	chr1:158575729-158575730
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	chr1:158573956..158576878-chr1:158587487..158590074,2	K562	blood:

Variant related genes	Relation type
ENSG00000163554	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1029083	0.87[EUR][1000 genomes]
rs16840314	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs2022002	0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2022003	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs2157691	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2246434	0.86[CEU][hapmap];0.91[GIH][hapmap];0.88[EUR][1000 genomes]
rs2251963	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2251964	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2479861	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2479862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2479868	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2482963	0.94[EUR][1000 genomes]
rs2518489	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2518490	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2518491	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2518493	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs2779116	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2852634	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2852635	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2852637	0.87[EUR][1000 genomes]
rs857683	1.00[ASN][1000 genomes]
rs857685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857686	1.00[ASN][1000 genomes]
rs857688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs857689	0.86[EUR][1000 genomes]
rs857691	0.84[EUR][1000 genomes]
rs857708	0.99[ASN][1000 genomes]
rs857719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs857720	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs857721	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs857725	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]
rs860772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs861409	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs863327	0.81[CEU][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs863343	0.85[CEU][hapmap]
rs863344	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs863366	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs863368	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][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

Variant related diseases (count:1)

Disease	PMID	Source
Red blood cell traits	23222517	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs857684	PYHIN1	cis	cerebellum	SCAN
rs857684	SLC27A3	cis	cerebellum	SCAN
rs857684	OR10Z1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158574000-158576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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