Variant report

Variant	rs7740062
Chromosome Location	chr6:27705598-27705599
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	chr6:27697073..27699346-chr6:27703837..27706008,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs16867858	0.84[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16867899	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs16867901	1.00[TSI][hapmap]
rs16867911	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs169263	0.84[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs187995	1.00[EUR][1000 genomes]
rs200470	1.00[EUR][1000 genomes]
rs200472	1.00[EUR][1000 genomes]
rs200483	0.86[MKK][hapmap]
rs200947	1.00[EUR][1000 genomes]
rs200955	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs200959	0.84[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs200968	0.89[MKK][hapmap]
rs200970	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs200982	1.00[EUR][1000 genomes]
rs200984	1.00[EUR][1000 genomes]
rs200995	0.89[MKK][hapmap]
rs201003	1.00[EUR][1000 genomes]
rs201005	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs56342784	1.00[EUR][1000 genomes]
rs59716769	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6904979	0.84[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9295739	1.00[TSI][hapmap]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]
rs9468228	0.83[YRI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv970372	chr6:27695204-27708579	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv981370	chr6:27696520-27708579	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7740062	SLC5A7	trans	brain	seeQTL
rs7740062	GSG1	trans	brain	seeQTL
rs7740062	SH2D2A	trans	brain	seeQTL
rs7740062	CRX	trans	brain	seeQTL
rs7740062	ASMT	trans	brain	seeQTL
rs7740062	OTX2	trans	brain	seeQTL
rs7740062	GUCA1C	trans	brain	seeQTL
rs7740062	TTR	trans	brain	seeQTL
rs7740062	PDE6H	trans	brain	seeQTL
rs7740062	Hs.158943	cis	multi-tissue	Pritchard
rs7740062	LRTM1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27702200-27706000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27704800-27705600	Enhancers	K562	blood
3	chr6:27705400-27705600	Flanking Active TSS	GM12878-XiMat	blood
4	chr6:27705400-27707400	Active TSS	A549	lung

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