Variant report

Variant	rs9380874
Chromosome Location	chr6:39486517-39486518
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	chr6:39481932..39484239-chr6:39485790..39487293,2	K562	blood:
2	chr6:39485932..39488385-chr6:39492203..39494440,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11751784	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11969059	0.84[CHB][hapmap]
rs1410487	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1546910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17457401	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927774	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs1927775	0.84[CHB][hapmap]
rs1952362	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs2026670	0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2073134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236064	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs4254985	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4446568	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4540261	0.89[CHB][hapmap]
rs4714256	0.84[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs55860200	0.82[ASN][1000 genomes]
rs56951565	0.86[ASN][1000 genomes]
rs58087685	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458117	0.80[MEX][hapmap]
rs6901155	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs6919556	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6922624	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6930913	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6942355	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9296298	0.90[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap]
rs9296300	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs9357306	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357307	0.84[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9357310	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9367008	0.84[CHB][hapmap]
rs9367009	0.84[CHB][hapmap]
rs9367014	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367015	0.89[ASN][1000 genomes]
rs9367017	0.86[ASN][1000 genomes]
rs9369119	0.89[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs9369122	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380863	0.84[CHB][hapmap]
rs9380868	0.82[CHB][hapmap]
rs9380875	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394599	0.84[CHB][hapmap]
rs9394610	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9462553	0.84[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9471113	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9471118	0.88[ASN][1000 genomes]
rs9471128	0.80[MEX][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	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9380874	CCND3	cis	cerebellum	SCAN
rs9380874	CRIP3	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39481200-39489800	Weak transcription	Pancreas	Pancrea
2	chr6:39485000-39493200	Enhancers	Fetal Lung	lung
3	chr6:39486000-39486600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:39486200-39488000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:39486200-39488200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:39486200-39488200	Weak transcription	NHDF-Ad	bronchial
7	chr6:39486200-39488400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:39486200-39498200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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