Variant report

Variant	rs7978448
Chromosome Location	chr12:49506940-49506941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr12:49506636-49507006	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49493937..49507579-chr12:49519161..49528577,46	K562	blood:
2	chr12:49506528..49509640-chr12:49657775..49661658,4	K562	blood:
3	chr12:49506887..49508867-chr12:49523655..49525938,3	MCF-7	breast:

Variant related genes	Relation type
LMBR1L	TF binding region
ENSG00000200309	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1039225	0.96[CEU][hapmap]
rs1057548	0.83[EUR][1000 genomes]
rs10747561	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747562	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783302	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783304	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783306	0.86[ASN][1000 genomes]
rs10783307	0.86[ASN][1000 genomes]
rs10783308	0.87[CEU][hapmap]
rs10875924	0.88[CEU][hapmap]
rs10875928	0.87[CEU][hapmap]
rs10875931	0.87[CEU][hapmap]
rs11168857	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168862	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168867	0.81[ASN][1000 genomes]
rs11168874	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168884	0.88[CEU][hapmap]
rs11168888	0.82[EUR][1000 genomes]
rs11168895	0.82[EUR][1000 genomes]
rs11168910	0.96[CEU][hapmap]
rs11837207	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12228775	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12229524	0.96[CEU][hapmap]
rs1476137	0.88[CEU][hapmap];0.92[ASN][1000 genomes]
rs1476138	0.85[ASN][1000 genomes]
rs1874908	0.87[CEU][hapmap]
rs1991427	0.96[CEU][hapmap]
rs2047101	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241727	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279596	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2334930	0.87[CEU][hapmap]
rs2753	0.87[CEU][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35884657	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741621	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57853986	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73110168	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs731350	0.87[CEU][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7954521	0.88[CEU][hapmap]
rs7954530	0.87[CEU][hapmap]
rs7957983	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957998	0.87[CEU][hapmap]
rs7958241	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958572	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959497	0.87[CEU][hapmap]
rs7969963	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969967	0.96[CEU][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7976890	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978659	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9325145	0.87[CEU][hapmap];0.92[ASN][1000 genomes]
rs9788139	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9788140	0.84[EUR][1000 genomes];0.91[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7978448	CCDC65	cis	Artery Aorta	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49505200-49507200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:49505200-49508000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:49505400-49508000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:49505400-49508000	Weak transcription	Osteobl	bone
5	chr12:49505400-49510800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:49505400-49510800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:49505400-49511000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:49505400-49514800	Weak transcription	HSMM	muscle
9	chr12:49505400-49521000	Weak transcription	Spleen	Spleen
10	chr12:49505600-49508000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:49506200-49507200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:49506400-49510400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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