Variant report

Variant	rs17773299
Chromosome Location	chr12:4500608-4500609
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	chr12:4487780..4490097-chr12:4499564..4501333,2	K562	blood:

Variant related genes	Relation type
ENSG00000118972	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11063105	0.86[ASN][1000 genomes]
rs11063110	0.86[ASN][1000 genomes]
rs11063112	0.94[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs11063116	0.82[EUR][1000 genomes]
rs11063118	0.88[CHB][hapmap]
rs11063123	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11063127	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11063129	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11063130	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230757	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs12823931	0.87[CHB][hapmap]
rs13312789	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16931344	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2358955	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61909253	0.82[ASN][1000 genomes]
rs61909254	0.82[ASN][1000 genomes]
rs6489538	0.98[ASN][1000 genomes]
rs7316649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7955866	0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7961824	0.84[ASN][1000 genomes]
rs7966472	0.85[ASN][1000 genomes]
rs7967051	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976548	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978281	0.80[EUR][1000 genomes];0.95[ASN][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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898616	chr12:4490059-4564613	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17773299	NECAP1	cis	cerebellum	SCAN
rs17773299	CDCA3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4498400-4501400	Weak transcription	Left Ventricle	heart
2	chr12:4499000-4501200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr12:4499800-4501200	Weak transcription	K562	blood
4	chr12:4500000-4501400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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