Variant report

Variant	rs285578
Chromosome Location	chr12:41950368-41950369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10506194	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10506196	0.81[CHB][hapmap]
rs10880084	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10880090	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10880097	0.91[JPT][hapmap]
rs10880101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10880102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11180970	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11180972	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11180973	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11180974	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11180975	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11180976	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11180978	0.91[JPT][hapmap]
rs11180983	0.84[JPT][hapmap]
rs11180989	0.91[JPT][hapmap]
rs11180995	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11180997	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11181000	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11181005	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11181010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11181012	0.91[ASN][1000 genomes]
rs11181013	0.91[ASN][1000 genomes]
rs11181015	0.91[ASN][1000 genomes]
rs11181019	0.87[ASN][1000 genomes]
rs11181020	0.87[ASN][1000 genomes]
rs11181023	0.87[ASN][1000 genomes]
rs11181025	0.82[ASN][1000 genomes]
rs12227303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12227540	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12230351	0.94[ASN][1000 genomes]
rs12582909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1458153	0.91[JPT][hapmap]
rs1458172	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1458173	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs157973	0.82[LWK][hapmap];0.87[MKK][hapmap]
rs17129470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17129528	0.91[ASN][1000 genomes]
rs17835484	0.90[JPT][hapmap]
rs2125289	0.90[JPT][hapmap]
rs285577	1.00[ASW][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.82[AFR][1000 genomes]
rs725527	0.91[JPT][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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs285578	NKAP	trans	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41942800-41956800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41944600-41966200	Weak transcription	Ovary	ovary
3	chr12:41945400-41956800	Weak transcription	Aorta	Aorta
4	chr12:41947200-41953000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:41948600-41959800	Weak transcription	Brain Germinal Matrix	brain
6	chr12:41949800-41952400	Strong transcription	Stomach Smooth Muscle	stomach
7	chr12:41950200-41950400	Enhancers	Fetal Lung	lung

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