Variant report

Variant	rs6665090
Chromosome Location	chr1:78688656-78688657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78688515..78690733-chr1:78694241..78696513,2	K562	blood:

Variant related genes	Relation type
ENSG00000237413	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11162433	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11162435	0.80[ASN][1000 genomes]
rs11162436	0.80[ASN][1000 genomes]
rs1323097	0.80[ASN][1000 genomes]
rs1323099	0.82[ASN][1000 genomes]
rs1407747	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1407748	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1625234	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1745624	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1770307	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2181453	0.82[ASN][1000 genomes]
rs4258184	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4285658	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4650607	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4650639	0.84[ASN][1000 genomes]
rs582795	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs589683	0.91[ASN][1000 genomes]
rs591206	0.90[ASN][1000 genomes]
rs591343	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs597063	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs597272	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs610508	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs614836	0.93[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs618063	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs618581	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs633664	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs634741	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs637650	0.99[ASN][1000 genomes]
rs644332	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs646971	0.92[ASN][1000 genomes]
rs647809	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs648315	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659902	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs666897	0.90[ASN][1000 genomes]
rs675799	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs677875	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs679843	0.89[ASN][1000 genomes]
rs680971	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs681907	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs683097	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs684996	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs720579	0.89[ASN][1000 genomes]
rs7540033	0.89[ASN][1000 genomes]
rs809911	0.85[AFR][1000 genomes]
rs942100	0.91[ASN][1000 genomes]
rs9425188	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6665090	DNAJB4	cis	parietal	SCAN
rs6665090	LHX8	cis	parietal	SCAN
rs6665090	NEXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78687800-78689000	Weak transcription	Gastric	stomach
2	chr1:78687800-78689000	Weak transcription	Pancreas	Pancrea
3	chr1:78688000-78691200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:78688000-78691400	Enhancers	Hela-S3	cervix
5	chr1:78688200-78689200	Flanking Active TSS	Liver	Liver
6	chr1:78688200-78690000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:78688400-78689600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:78688400-78689600	Enhancers	HMEC	breast
9	chr1:78688400-78689800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:78688400-78690200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:78688400-78690400	Enhancers	Osteobl	bone
12	chr1:78688600-78689800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:78688600-78689800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:78688600-78689800	Enhancers	Placenta Amnion	Placenta Amnion

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