Variant report

Variant	rs325220
Chromosome Location	chr5:98304564-98304565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98262647..98265135-chr5:98302545..98304795,4	K562	blood:
2	chr5:98304057..98306141-chr5:98308970..98311367,2	K562	blood:
3	chr5:98262647..98265058-chr5:98302545..98304795,3	K562	blood:
4	chr5:98297682..98299622-chr5:98302405..98305273,3	K562	blood:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10037147	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10038192	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10040066	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10050423	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10076291	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10477857	0.93[ASN][1000 genomes]
rs10479344	0.81[AMR][1000 genomes]
rs10479345	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10479346	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10479348	0.81[ASN][1000 genomes]
rs1093794	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1104262	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11242567	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs11949103	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950452	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950855	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11960896	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12109067	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12189335	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13179812	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1393210	0.84[EUR][1000 genomes]
rs1472622	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs150992	0.83[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs151102	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs161729	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs161730	0.98[ASN][1000 genomes]
rs161731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161732	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs161735	0.83[CEU][hapmap]
rs161740	0.83[CEU][hapmap]
rs161747	0.83[CEU][hapmap]
rs161935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161936	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161948	0.81[EUR][1000 genomes]
rs161950	0.83[CEU][hapmap]
rs161952	0.83[CEU][hapmap]
rs162337	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs162341	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167798	0.98[ASN][1000 genomes]
rs172874	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875529	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2221268	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2455423	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927647	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2927648	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2927654	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937706	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937708	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937709	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs325195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs326480	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs326481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs326482	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs326493	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs327811	0.84[MEX][hapmap];0.88[TSI][hapmap]
rs330419	0.83[CEU][hapmap]
rs331929	0.83[CEU][hapmap]
rs34488	0.98[ASN][1000 genomes]
rs34489	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34490	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34491	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34497	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs34499	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs363929	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs366000	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs366353	1.00[CHB][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370529	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs378089	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380156	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393697	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs395668	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398436	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs407562	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs416750	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs422127	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs428836	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434039	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443726	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4448016	0.83[EUR][1000 genomes]
rs447044	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs449204	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs451141	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4565239	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4583911	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs45931	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs467728	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs469018	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4703048	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4703049	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4703051	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4703052	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703340	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs539024	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs559574	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6865618	0.83[EUR][1000 genomes]
rs6878136	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6885458	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs692832	0.83[CEU][hapmap]
rs709386	0.93[ASN][1000 genomes]
rs709387	0.93[ASN][1000 genomes]
rs709388	0.93[ASN][1000 genomes]
rs709389	0.93[ASN][1000 genomes]
rs709390	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7710032	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7711061	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7719562	1.00[CHB][hapmap]
rs819227	0.93[ASN][1000 genomes]
rs819230	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs819231	0.93[ASN][1000 genomes]
rs819232	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs325220	SLCO4C1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98301600-98305400	Weak transcription	K562	blood

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