Variant report

Variant	rs2701684
Chromosome Location	chr7:107299527-107299528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr7:107299220-107301021	K562	blood:	n/a	chr7:107300858-107300870

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:107298440..107300268-chr7:107301812..107303689,2	K562	blood:
2	chr7:107297566..107299940-chr7:107300872..107303312,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COG5-1	chr7:107297075-107300651	ENSG00000233705
2	lnc-COG5-1	chr7:107296961-107300651	NONHSAT122700

Variant related genes	Relation type
SLC26A4	TF binding region
ENSG00000233705	Chromatin interaction
ENSG00000091137	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1015411	0.87[CEU][hapmap]
rs10258385	0.91[CEU][hapmap]
rs10267907	0.86[CEU][hapmap]
rs10273733	0.91[CEU][hapmap]
rs10274041	0.91[CEU][hapmap]
rs10276604	0.91[CEU][hapmap]
rs10281535	0.91[CEU][hapmap]
rs11771278	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11977187	0.91[CEU][hapmap]
rs12673675	0.87[CEU][hapmap]
rs13228252	0.89[ASN][1000 genomes]
rs2057837	0.91[CEU][hapmap]
rs2066735	0.87[CEU][hapmap]
rs2107713	0.91[CEU][hapmap]
rs2178497	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs2237677	0.87[CEU][hapmap]
rs2248465	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2253146	0.87[CEU][hapmap]
rs2253269	0.82[CEU][hapmap]
rs2253271	0.86[CEU][hapmap]
rs2395907	0.91[CEU][hapmap]
rs2520241	0.87[CEU][hapmap]
rs2520242	0.87[CEU][hapmap]
rs2520243	0.82[CEU][hapmap]
rs2520245	0.82[CEU][hapmap]
rs2520249	0.87[CEU][hapmap]
rs2520268	0.91[CEU][hapmap]
rs2520269	0.82[CEU][hapmap]
rs2701678	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2701679	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2701685	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2701687	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2712201	0.87[CEU][hapmap]
rs2712227	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2712228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712229	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808	0.91[CEU][hapmap]
rs2894466	0.91[CEU][hapmap]
rs2894475	0.91[CEU][hapmap]
rs3094383	0.86[CEU][hapmap]
rs3801944	0.91[CEU][hapmap]
rs3801948	0.91[CEU][hapmap]
rs4727684	0.91[CEU][hapmap]
rs6976607	0.91[CEU][hapmap]
rs7778250	0.91[CEU][hapmap]
rs7778270	0.91[CEU][hapmap]
rs7793613	0.91[CEU][hapmap]
rs7803102	0.91[CEU][hapmap]
rs986994	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2701684	GPR22	cis	multi-tissue	Pritchard
rs2701684	COG5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107298600-107300800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:107298800-107300200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:107299200-107301200	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr7:107299400-107301800	Enhancers	Dnd41	blood

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