Variant report

Variant	rs9869638
Chromosome Location	chr3:102460575-102460576
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:102391655..102393123-chr3:102459418..102460722,10	MCF-7	breast:
2	chr3:102189575..102190143-chr3:102459670..102460629,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241754	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11707739	0.80[ASN][1000 genomes]
rs11720453	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1241144	0.89[ASN][1000 genomes]
rs1241153	0.86[ASN][1000 genomes]
rs12486666	0.93[ASN][1000 genomes]
rs1263031	0.86[ASN][1000 genomes]
rs1271234	0.86[ASN][1000 genomes]
rs13084671	0.86[ASN][1000 genomes]
rs1353692	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1354727	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1397909	0.89[ASN][1000 genomes]
rs1474186	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1498070	0.86[ASN][1000 genomes]
rs1498086	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1498089	0.89[ASN][1000 genomes]
rs1506436	0.80[ASN][1000 genomes]
rs1589287	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1609976	0.80[ASN][1000 genomes]
rs1694183	0.82[ASN][1000 genomes]
rs1694185	0.82[ASN][1000 genomes]
rs1705928	0.82[ASN][1000 genomes]
rs1715542	0.80[ASN][1000 genomes]
rs1715546	0.80[ASN][1000 genomes]
rs1715547	0.80[ASN][1000 genomes]
rs1715553	0.80[ASN][1000 genomes]
rs1715554	0.80[ASN][1000 genomes]
rs17831612	0.94[ASN][1000 genomes]
rs1912798	0.86[ASN][1000 genomes]
rs2088475	0.93[ASN][1000 genomes]
rs2173329	0.86[ASN][1000 genomes]
rs2398774	0.86[ASN][1000 genomes]
rs2971239	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs34116120	0.93[ASN][1000 genomes]
rs3914180	0.86[ASN][1000 genomes]
rs4856063	0.86[ASN][1000 genomes]
rs4856112	0.80[AMR][1000 genomes]
rs4856149	0.93[ASN][1000 genomes]
rs55635554	0.93[ASN][1000 genomes]
rs6441671	0.93[ASN][1000 genomes]
rs6768201	0.93[ASN][1000 genomes]
rs6768503	0.93[ASN][1000 genomes]
rs6770963	0.93[ASN][1000 genomes]
rs6800928	0.89[ASN][1000 genomes]
rs73137731	0.89[ASN][1000 genomes]
rs73137742	0.98[ASN][1000 genomes]
rs73139703	0.94[ASN][1000 genomes]
rs73139709	0.94[ASN][1000 genomes]
rs7431663	0.86[ASN][1000 genomes]
rs7610030	0.86[ASN][1000 genomes]
rs7613307	0.86[ASN][1000 genomes]
rs7614921	0.86[ASN][1000 genomes]
rs825345	0.86[ASN][1000 genomes]
rs825347	0.86[ASN][1000 genomes]
rs825356	0.89[ASN][1000 genomes]
rs825357	0.83[ASN][1000 genomes]
rs825358	0.86[ASN][1000 genomes]
rs825360	0.85[ASN][1000 genomes]
rs825361	0.85[ASN][1000 genomes]
rs9290744	0.80[ASN][1000 genomes]
rs931652	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs939326	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs953281	0.86[ASN][1000 genomes]
rs9810913	0.93[ASN][1000 genomes]
rs9815206	0.86[ASN][1000 genomes]
rs9844846	0.80[ASN][1000 genomes]
rs9866969	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882411	0.86[ASN][1000 genomes]
rs9883402	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007340	chr3:102108954-102725099	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv536676	chr3:102108954-102725099	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1009392	chr3:102199756-102631205	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv877228	chr3:102345638-102751470	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv591190	chr3:102345638-102946216	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834776	chr3:102351486-102532042	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1000584	chr3:102358773-102923378	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv915978	chr3:102386795-102949530	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv877229	chr3:102415127-102649650	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv877230	chr3:102457118-102635852	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1013012	chr3:102458158-102587883	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9869638	FAM172B	cis	parietal	SCAN
rs9869638	OR7G2	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:102453800-102460600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:102459400-102460600	Enhancers	Fetal Heart	heart
3	chr3:102460000-102460800	Enhancers	Liver	Liver
4	chr3:102460200-102460800	Enhancers	Ovary	ovary

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