Variant report

Variant	rs13312789
Chromosome Location	chr12:4481044-4481045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11063105	0.96[ASN][1000 genomes]
rs11063110	0.96[ASN][1000 genomes]
rs11063112	0.93[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap];0.94[ASN][1000 genomes]
rs11063116	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11063118	0.87[CHB][hapmap]
rs11063123	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11063127	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11063129	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11063130	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12229274	0.83[AFR][1000 genomes]
rs12230757	0.82[ASW][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.88[ASN][1000 genomes]
rs12823931	0.86[CHB][hapmap];0.85[LWK][hapmap]
rs16931344	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17773299	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]
rs2358955	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812822	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61909253	0.81[ASN][1000 genomes]
rs61909254	0.81[ASN][1000 genomes]
rs6489538	0.92[ASN][1000 genomes]
rs7133330	0.80[LWK][hapmap]
rs7316649	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7955866	0.82[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961824	0.94[ASN][1000 genomes]
rs7966472	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7967051	0.89[ASN][1000 genomes]
rs7976548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978281	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13312789	NECAP1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4465200-4488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:4478600-4484200	Strong transcription	Fetal Intestine Large	intestine
3	chr12:4480400-4484400	Weak transcription	Fetal Intestine Small	intestine

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