Variant report

Variant	rs7955866
Chromosome Location	chr12:4479549-4479550
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	chr12:4474863..4476758-chr12:4478306..4479847,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11063105	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11063110	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11063112	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11063116	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11063118	0.82[CHB][hapmap]
rs11063123	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11063127	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11063129	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11063130	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12230757	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12823931	0.94[CHB][hapmap];0.95[LWK][hapmap]
rs13312789	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]
rs16931344	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17773299	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]
rs2358955	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812822	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6489538	0.88[ASN][1000 genomes]
rs7133330	0.89[LWK][hapmap]
rs7316649	0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961824	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7966472	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7967051	0.86[ASN][1000 genomes]
rs7976548	0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978281	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[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
rs7955866	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	chr12:4479400-4480400	Strong transcription	Fetal Intestine Small	intestine

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