Variant report

Variant	rs10489066
Chromosome Location	chr4:16292409-16292410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16292192..16292811-chr4:16446518..16447107,2	MCF-7	breast:
2	chr4:16291175..16292655-chr4:16444905..16445780,4	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10489059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489060	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501129	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16893241	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16893297	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801072	0.81[EUR][1000 genomes]
rs1860822	0.92[EUR][1000 genomes]
rs2215639	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484297	0.91[ASN][1000 genomes]
rs4574401	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828272	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6851339	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6851785	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73224549	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73234672	0.87[EUR][1000 genomes]
rs73234682	0.87[EUR][1000 genomes]
rs73234684	0.87[EUR][1000 genomes]
rs73234692	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73234694	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73234696	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73234701	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235977	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235978	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235995	0.93[EUR][1000 genomes]
rs73238006	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239725	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239728	0.89[EUR][1000 genomes]
rs73239730	0.92[EUR][1000 genomes]
rs73239731	0.92[EUR][1000 genomes]
rs73239734	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239736	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73239737	0.92[EUR][1000 genomes]
rs73239739	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239740	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239743	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239747	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239749	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239751	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239758	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239760	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239761	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73239765	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239766	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239768	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239769	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239771	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239772	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239773	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239774	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239777	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685190	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489066	FLJ39653	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16291400-16293400	Enhancers	Fetal Kidney	kidney
2	chr4:16291600-16293200	Enhancers	Adipose Nuclei	Adipose
3	chr4:16291800-16293000	Bivalent Enhancer	HUVEC	blood vessel
4	chr4:16291800-16293200	Enhancers	Fetal Brain Male	brain
5	chr4:16291800-16293400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr4:16292000-16292600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:16292000-16292600	Enhancers	Fetal Muscle Leg	muscle
8	chr4:16292000-16293000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:16292200-16292600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:16292200-16292600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:16292200-16292600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:16292200-16292600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr4:16292200-16292600	Enhancers	Stomach Mucosa	stomach
14	chr4:16292200-16293000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr4:16292200-16293800	Weak transcription	Fetal Stomach	stomach
16	chr4:16292200-16296000	Weak transcription	NHDF-Ad	bronchial
17	chr4:16292400-16292600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:16292400-16292600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr4:16292400-16295800	Weak transcription	Osteobl	bone

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