Variant report

Variant	rs6580649
Chromosome Location	chr12:48410517-48410518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48395740..48398491-chr12:48410326..48412487,2	MCF-7	breast:
2	chr12:48407751..48410923-chr12:48414618..48417182,4	MCF-7	breast:
3	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
4	chr12:48409071..48411163-chr12:48439800..48441969,2	MCF-7	breast:
5	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1018973	0.81[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs1034762	0.81[CEU][hapmap]
rs10492080	0.92[TSI][hapmap]
rs10783226	0.85[EUR][1000 genomes]
rs10783227	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11612578	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs11612970	0.83[EUR][1000 genomes]
rs11613485	0.81[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs12580764	0.85[EUR][1000 genomes]
rs12581972	0.82[EUR][1000 genomes]
rs1476608	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs1635526	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1635529	0.81[EUR][1000 genomes]
rs17122611	0.85[EUR][1000 genomes]
rs17122612	0.81[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs17122613	0.84[EUR][1000 genomes]
rs17122651	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs1793931	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs1793933	0.93[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs1793955	0.82[EUR][1000 genomes]
rs1859441	0.87[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1859444	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1968071	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs1990029	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286022	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3742074	0.81[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs3803183	0.90[EUR][1000 genomes]
rs3803184	0.90[EUR][1000 genomes]
rs3825404	1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4293182	0.83[EUR][1000 genomes]
rs4760611	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs4760614	0.91[EUR][1000 genomes]
rs4760615	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760618	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760620	0.88[TSI][hapmap]
rs4760677	0.91[EUR][1000 genomes]
rs4760683	0.88[TSI][hapmap]
rs57380031	0.84[EUR][1000 genomes]
rs59766465	0.84[EUR][1000 genomes]
rs60629297	0.84[EUR][1000 genomes]
rs60681522	0.85[EUR][1000 genomes]
rs6580647	1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs6580651	0.91[EUR][1000 genomes]
rs7132668	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7133249	0.85[EUR][1000 genomes]
rs726354	0.92[TSI][hapmap]
rs72644841	0.94[EUR][1000 genomes]
rs72644842	0.91[EUR][1000 genomes]
rs72644843	0.85[EUR][1000 genomes]
rs72644844	0.85[EUR][1000 genomes]
rs7296913	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs7305954	0.88[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs7310579	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7315258	0.88[TSI][hapmap]
rs7957764	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7959755	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs7967762	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7971668	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs917055	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs9651993	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9805048	0.88[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580649	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48407600-48411400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:48407800-48410800	Weak transcription	Fetal Intestine Small	intestine
4	chr12:48408800-48410600	Weak transcription	Fetal Intestine Large	intestine
5	chr12:48409200-48410600	Enhancers	Hela-S3	cervix
6	chr12:48410000-48410600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:48410200-48410600	Bivalent Enhancer	HepG2	liver
8	chr12:48410200-48411400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48410200-48411600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48410200-48411600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:48410400-48410600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:48410400-48410600	Bivalent Enhancer	HUVEC	blood vessel
13	chr12:48410400-48411000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:48410400-48411200	Enhancers	HMEC	breast
15	chr12:48410400-48411400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:48410400-48411600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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