Variant report

Variant	rs1474879
Chromosome Location	chr20:1386473-1386474
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	chr20:1384990..1387871-chr20:1389849..1391425,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11696447	1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11699494	1.00[CHB][hapmap]
rs12481707	1.00[JPT][hapmap]
rs13163	1.00[CHB][hapmap]
rs1474880	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap]
rs16995310	1.00[CHB][hapmap]
rs16995332	1.00[CHB][hapmap]
rs17793360	1.00[JPT][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1884393	1.00[JPT][hapmap]
rs2064645	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2064646	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2273321	1.00[JPT][hapmap]
rs2873522	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3829697	1.00[JPT][hapmap]
rs41308086	1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs58194712	1.00[ASN][1000 genomes]
rs58718584	1.00[ASN][1000 genomes]
rs59239479	1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042506	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042574	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	1.00[ASN][1000 genomes]
rs6109437	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109522	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109837	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6109986	1.00[ASN][1000 genomes]
rs6109989	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6109992	1.00[ASN][1000 genomes]
rs6110189	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110193	1.00[CHB][hapmap]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs66497853	1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8117563	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8118276	1.00[CHB][hapmap]
rs8118710	1.00[JPT][hapmap]
rs8124855	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]
rs959813	1.00[ASN][1000 genomes]
rs984497	1.00[JPT][hapmap]
rs984498	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv994443	chr20:1385239-1392933	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1474879	DEFB132	cis	cerebellum	SCAN
rs1474879	TCF15	cis	cerebellum	SCAN
rs1474879	CDS2	cis	cerebellum	SCAN
rs1474879	SNRPB	cis	cerebellum	SCAN
rs1474879	FKBP1A	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1380600-1388400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr20:1382400-1388400	Weak transcription	Placenta	Placenta
3	chr20:1383200-1388000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr20:1383800-1396000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:1384400-1395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:1384400-1396000	Weak transcription	HMEC	breast
7	chr20:1385600-1387800	Enhancers	Fetal Intestine Large	intestine
8	chr20:1385800-1387600	Enhancers	Fetal Intestine Small	intestine

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