Variant report

Variant	rs6930913
Chromosome Location	chr6:39508795-39508796
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	chr6:39508684..39511349-chr6:39512535..39516562,4	MCF-7	breast:
2	chr6:39507475..39509362-chr6:39510775..39512665,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11751784	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12664369	0.80[CHB][hapmap]
rs1328387	0.90[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs1410487	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1546910	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17457401	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2026670	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs2073134	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736735	0.80[CHB][hapmap]
rs4236064	0.83[JPT][hapmap]
rs4254985	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4446568	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714256	0.83[JPT][hapmap]
rs56951565	0.81[ASN][1000 genomes]
rs58087685	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458117	0.90[ASW][hapmap];0.80[LWK][hapmap];0.82[MKK][hapmap];0.81[AMR][1000 genomes]
rs6901155	0.84[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs6907077	0.81[AMR][1000 genomes]
rs6919556	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6922624	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6942355	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296298	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs9296300	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9357306	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357307	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9357310	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9367014	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9367015	0.84[ASN][1000 genomes]
rs9367017	0.81[ASN][1000 genomes]
rs9369119	0.83[JPT][hapmap]
rs9369122	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380874	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]
rs9380875	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380877	0.80[CHB][hapmap]
rs9380880	0.80[CHB][hapmap]
rs9394608	0.80[CHB][hapmap]
rs9394609	0.80[CHB][hapmap]
rs9394610	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394611	0.80[CHB][hapmap]
rs9462553	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9471113	0.82[JPT][hapmap]
rs9471118	0.82[ASN][1000 genomes]
rs9471128	0.90[ASW][hapmap];0.80[LWK][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6930913	CRIP3	cis	cerebellum	SCAN
rs6930913	CCND3	cis	cerebellum	SCAN
rs6930913	KCNK17	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39488600-39509400	Weak transcription	Brain Substantia Nigra	brain
2	chr6:39495200-39511000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:39498400-39509400	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:39498600-39510600	Weak transcription	Rectal Smooth Muscle	rectum

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