Variant report

Variant	rs857723
Chromosome Location	chr1:158604000-158604001
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	chr1:158595251..158598150-chr1:158602419..158604150,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1032352	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10489833	0.88[CEU][hapmap]
rs10797020	0.88[CEU][hapmap]
rs10797022	0.83[EUR][1000 genomes]
rs10797023	0.83[EUR][1000 genomes]
rs10797024	0.83[EUR][1000 genomes]
rs10908656	0.88[CEU][hapmap]
rs10908663	0.84[EUR][1000 genomes]
rs11265003	0.88[CEU][hapmap]
rs1157525	0.85[CEU][hapmap]
rs12118446	0.83[EUR][1000 genomes]
rs12122663	0.84[EUR][1000 genomes]
rs12133791	0.84[EUR][1000 genomes]
rs12133794	0.83[EUR][1000 genomes]
rs12145401	0.83[EUR][1000 genomes]
rs12601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1332699	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1342947	0.88[CEU][hapmap]
rs1557615	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1578761	0.83[EUR][1000 genomes]
rs1578762	0.83[EUR][1000 genomes]
rs1578763	0.83[EUR][1000 genomes]
rs1873509	0.88[CEU][hapmap]
rs1873510	0.88[CEU][hapmap]
rs1873511	0.88[CEU][hapmap]
rs1894040	0.88[CEU][hapmap]
rs2157687	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2188111	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2251969	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2317969	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2317970	0.84[EUR][1000 genomes]
rs2479867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2852636	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2873593	0.84[EUR][1000 genomes]
rs2873594	0.84[EUR][1000 genomes]
rs2873595	0.84[EUR][1000 genomes]
rs4276920	0.84[EUR][1000 genomes]
rs4575081	0.84[EUR][1000 genomes]
rs4609418	0.88[CEU][hapmap]
rs6657638	0.83[EUR][1000 genomes]
rs6663277	0.83[EUR][1000 genomes]
rs6666609	0.84[EUR][1000 genomes]
rs6670343	0.83[EUR][1000 genomes]
rs6672789	0.83[EUR][1000 genomes]
rs6674656	0.83[EUR][1000 genomes]
rs6697656	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6699473	0.83[EUR][1000 genomes]
rs7512592	0.88[CEU][hapmap]
rs7514968	0.83[EUR][1000 genomes]
rs7515245	0.83[EUR][1000 genomes]
rs7518708	0.84[EUR][1000 genomes]
rs7518808	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs7525362	0.83[EUR][1000 genomes]
rs7533071	0.84[EUR][1000 genomes]
rs7540999	0.84[EUR][1000 genomes]
rs7548349	0.83[EUR][1000 genomes]
rs7549581	0.95[CEU][hapmap]
rs7555174	0.80[EUR][1000 genomes]
rs857676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs857677	0.82[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs857687	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs857716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857718	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857724	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs863931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs923663	0.84[EUR][1000 genomes]
rs923664	0.84[EUR][1000 genomes]
rs950260	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs950487	0.88[CEU][hapmap]
rs952094	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

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
rs857723	SPRR2A	cis	parietal	SCAN
rs857723	DCST2	cis	cerebellum	SCAN
rs857723	CD5L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158583600-158607600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:158590400-158607400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:158603800-158610200	Strong transcription	K562	blood

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