Variant report

Variant	rs909977
Chromosome Location	chr6:133015041-133015042
allele	C/T
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	RAD21	chr6:133014954-133015348	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr6:133014608-133015050	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:133014655-133015145	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133014677..133015377-chr6:133088872..133089774,2	MCF-7	breast:

Variant related genes	Relation type
CCNG1P1	TF binding region

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

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1044593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1073954	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12195735	0.82[CEU][hapmap];0.88[TSI][hapmap]
rs2050154	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2223613	0.94[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2247269	0.91[CEU][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2247284	0.91[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2247285	0.91[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2251449	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2251455	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2262437	0.91[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2262438	0.88[ASW][hapmap];0.91[CEU][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2300077	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2327275	0.89[EUR][1000 genomes]
rs2745426	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745427	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745429	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2745430	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745431	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs2745435	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2745436	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2745437	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2745439	0.91[CEU][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2745440	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745441	0.88[ASW][hapmap];0.91[CEU][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2745442	0.88[ASW][hapmap];0.91[CEU][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2745443	0.91[CEU][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs2745444	0.95[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745445	0.94[CEU][hapmap];0.87[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2840812	0.89[ASN][1000 genomes]
rs2840813	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2840815	0.90[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840816	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840817	0.90[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2840818	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840819	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2840820	0.88[ASW][hapmap];0.91[CEU][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840821	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840822	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840823	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840824	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840825	0.95[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs2840826	0.91[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs3798792	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs3823026	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4897600	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4897604	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4897605	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897609	0.80[EUR][1000 genomes]
rs4897612	0.87[CEU][hapmap]
rs6936833	0.91[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs6938196	0.89[EUR][1000 genomes]
rs6941705	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs742516	0.82[ASW][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs7742200	0.80[EUR][1000 genomes]
rs909975	0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9389027	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9399038	0.91[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs990499	0.91[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs990500	0.91[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs909977	VNN1	cis	Whole Blood	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133004800-133016400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:133008800-133016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:133010400-133015200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:133011000-133015200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:133011800-133017200	Weak transcription	Spleen	Spleen
6	chr6:133014600-133015400	Genic enhancers	Liver	Liver
7	chr6:133014800-133015200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:133014800-133015200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr6:133015000-133015200	Enhancers	Stomach Mucosa	stomach
10	chr6:133015000-133017800	Weak transcription	Primary monocytes fromperipheralblood	blood

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