Variant report

Variant	rs2026670
Chromosome Location	chr6:39409237-39409238
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	chr6:39408141..39410215-chr6:39548515..39550672,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11962587	0.83[CHB][hapmap]
rs1410487	0.83[GIH][hapmap]
rs1410488	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1546910	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs16892158	0.83[CHB][hapmap]
rs17457401	0.82[ASN][1000 genomes]
rs1927774	0.88[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1927775	0.94[CHB][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs1952362	0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs2073134	0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2273063	0.80[CHD][hapmap]
rs2395727	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4236064	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs4540261	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs4711598	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs4714253	0.89[CHB][hapmap]
rs4714254	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4714255	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs4714256	0.89[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs55860200	0.88[ASN][1000 genomes]
rs58087685	0.82[ASN][1000 genomes]
rs6901155	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs6919556	0.80[CHB][hapmap];0.87[GIH][hapmap]
rs6922624	0.83[GIH][hapmap]
rs6930913	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs9296298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap]
rs9296299	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs9296300	0.84[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs9349120	0.89[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs9357306	0.83[ASN][1000 genomes]
rs9367014	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9369117	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9369119	0.83[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs9369122	0.80[CHB][hapmap];0.87[GIH][hapmap]
rs9380862	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9380863	0.94[CHB][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9380864	0.89[CHB][hapmap]
rs9380865	0.89[CHB][hapmap]
rs9380868	0.81[CHB][hapmap]
rs9380874	0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9394592	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs9394594	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs9394595	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs9394599	0.89[CHD][hapmap]
rs9394610	0.80[GIH][hapmap]
rs9462553	0.83[JPT][hapmap]
rs9471103	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9471105	0.82[ASW][hapmap];0.87[LWK][hapmap];0.96[YRI][hapmap]
rs9471113	0.89[CHB][hapmap];0.94[JPT][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	nsv428145	chr6:39404129-39460795	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2026670	C17orf80	trans	parietal	SCAN
rs2026670	CCND3	cis	cerebellum	SCAN
rs2026670	KCNK16	cis	parietal	SCAN
rs2026670	KCNK17	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39409200-39410000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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