Variant report

Variant	rs869938
Chromosome Location	chr9:1053308-1053309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:1052914..1055179-chr9:1057328..1059620,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12350001	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4741030	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7848572	0.81[EUR][1000 genomes]
rs869939	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872343	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025492	chr9:478813-1157169	Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv539897	chr9:478813-1157169	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv613037	chr9:643453-1138368	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv817248	chr9:706283-1457665	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv892010	chr9:841152-1069663	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1034070	chr9:911265-1152351	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1016222	chr9:999390-1284180	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1025752	chr9:1003311-1124524	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1027466	chr9:1007196-1097053	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1033117	chr9:1007196-1129306	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1016321	chr9:1034594-1592366	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv539908	chr9:1034594-1592366	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv948914	chr9:1050981-1311310	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:1049600-1053400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
2	chr9:1050000-1053400	Bivalent/Poised TSS	Thymus	Thymus
3	chr9:1051200-1053400	Bivalent Enhancer	Spleen	Spleen
4	chr9:1051600-1053400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
5	chr9:1052200-1053800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
6	chr9:1052200-1053800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
7	chr9:1052200-1054000	Bivalent/Poised TSS	Fetal Thymus	thymus
8	chr9:1052400-1053400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr9:1052400-1053800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
10	chr9:1052400-1054200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:1052600-1054200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:1053000-1053400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr9:1053000-1053400	Bivalent Enhancer	Right Ventricle	heart
14	chr9:1053000-1054400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr9:1053000-1054400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:1053200-1053400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:1053200-1053400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
18	chr9:1053200-1053400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
19	chr9:1053200-1053600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
20	chr9:1053200-1053600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
21	chr9:1053200-1053800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:1053200-1053800	Bivalent Enhancer	Brain Substantia Nigra	brain
23	chr9:1053200-1054400	Bivalent Enhancer	Brain Cingulate Gyrus	brain

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