Variant report

Variant	rs857721
Chromosome Location	chr1:158612548-158612549
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1029083	0.83[EUR][1000 genomes]
rs16840314	0.86[CEU][hapmap]
rs2022002	0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2022003	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]
rs2157691	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246434	0.86[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[EUR][1000 genomes]
rs2251963	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251964	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2479861	0.83[CHB][hapmap]
rs2479862	0.83[CHB][hapmap]
rs2479868	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2482963	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2518489	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518490	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518491	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518493	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2779116	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2852634	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2852635	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2852637	0.83[EUR][1000 genomes]
rs857684	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs857685	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs857688	0.83[CHB][hapmap]
rs857689	0.84[EUR][1000 genomes]
rs857719	0.83[CHB][hapmap]
rs857720	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857725	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];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs861409	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs863327	0.81[CEU][hapmap];0.90[MEX][hapmap];0.84[EUR][1000 genomes]
rs863343	0.85[CEU][hapmap]
rs863344	0.86[CEU][hapmap]
rs863366	0.83[CHB][hapmap]
rs863368	0.83[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

Variant related diseases (count:1)

Disease	PMID	Source
Other erythrocyte phenotypes	19862010	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs857721	SLC27A3	cis	cerebellum	SCAN
rs857721	OR10Z1	cis	cerebellum	SCAN
rs857721	PYHIN1	cis	cerebellum	SCAN
rs857721	SCAMP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158608400-158614000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:158611800-158618600	Weak transcription	Fetal Thymus	thymus
3	chr1:158612200-158628800	Strong transcription	K562	blood
4	chr1:158612400-158613400	Strong transcription	Primary hematopoietic stem cells	blood

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