Variant report

Variant	rs6479421
Chromosome Location	chr9:95190598-95190599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95189255..95191754-chr9:95431690..95434514,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10120210	1.00[YRI][hapmap]
rs10125510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058726	0.88[EUR][1000 genomes]
rs1058751	0.88[EUR][1000 genomes]
rs10733744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144933	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1152760	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1152761	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1152762	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1175737	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1175923	0.88[EUR][1000 genomes]
rs1175929	0.82[EUR][1000 genomes]
rs1175930	0.88[EUR][1000 genomes]
rs1175931	0.81[CEU][hapmap]
rs11787696	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11789578	0.91[EUR][1000 genomes]
rs11792542	0.88[EUR][1000 genomes]
rs11793505	0.88[EUR][1000 genomes]
rs11794966	0.84[EUR][1000 genomes]
rs12555097	0.82[EUR][1000 genomes]
rs1536423	1.00[YRI][hapmap]
rs2084289	0.88[EUR][1000 genomes]
rs2131918	1.00[YRI][hapmap]
rs2295939	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2296665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs230223	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2398749	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280213	0.91[EUR][1000 genomes]
rs41280215	0.91[EUR][1000 genomes]
rs472163	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs4743867	0.88[EUR][1000 genomes]
rs4743868	0.93[CEU][hapmap];0.86[GIH][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs4743871	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4744124	0.88[EUR][1000 genomes]
rs4744125	0.88[EUR][1000 genomes]
rs501814	0.90[EUR][1000 genomes]
rs557066	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs55894730	0.91[EUR][1000 genomes]
rs56374228	0.91[EUR][1000 genomes]
rs7042199	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895639	0.93[CEU][hapmap];0.86[GIH][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs9409464	0.91[EUR][1000 genomes]
rs9409465	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs9409466	0.81[CEU][hapmap]
rs9409467	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409469	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9409659	0.91[EUR][1000 genomes]
rs9409660	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409661	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409662	0.89[EUR][1000 genomes]
rs9409665	0.93[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9409666	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs944949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886781	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6479421	C9orf79	cis	parietal	SCAN
rs6479421	ANKRD19	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95186200-95202200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:95187000-95190600	Enhancers	Fetal Stomach	stomach
3	chr9:95187400-95192200	Weak transcription	Aorta	Aorta
4	chr9:95188400-95190800	Enhancers	Fetal Heart	heart
5	chr9:95189000-95194600	Weak transcription	NHDF-Ad	bronchial
6	chr9:95189400-95192200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:95189400-95192400	Weak transcription	Fetal Lung	lung
8	chr9:95189400-95194600	Weak transcription	Ovary	ovary
9	chr9:95189600-95194800	Weak transcription	Fetal Muscle Leg	muscle

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