Variant report

Variant	rs10117887
Chromosome Location	chr9:1047016-1047017
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	chr9:1044385..1047451-chr9:1048271..1050473,4	MCF-7	breast:
2	chr9:1007423..1009287-chr9:1045081..1047981,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMRT2-1	chr9:1046079-1047957	XLOC_007262
2	lnc-DMRT2-1	chr9:1046079-1047957	NONHSAT129961

Variant related genes	Relation type
ENSG00000173253	Chromatin interaction

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

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

rs_ID	r²[population]
rs10122013	1.00[EUR][1000 genomes]
rs10124800	1.00[EUR][1000 genomes]
rs10959157	1.00[EUR][1000 genomes]
rs12350938	1.00[EUR][1000 genomes]
rs73386599	1.00[EUR][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	nsv892013	chr9:943611-1047343	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:1044600-1047800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:1044800-1047600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr9:1044800-1047800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:1044800-1047800	Bivalent Enhancer	Fetal Stomach	stomach
5	chr9:1044800-1047800	Enhancers	Pancreas	Pancrea
6	chr9:1045800-1047400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:1045800-1047600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr9:1045800-1048000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:1046000-1047200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:1046000-1047400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
11	chr9:1046000-1047400	Weak transcription	Right Atrium	heart
12	chr9:1046200-1047200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:1046200-1047200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr9:1046200-1047400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr9:1046200-1047600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:1046200-1049000	Bivalent Enhancer	Spleen	Spleen
17	chr9:1046400-1047200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:1046400-1047200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
19	chr9:1046600-1047400	Bivalent Enhancer	Colonic Mucosa	Colon
20	chr9:1046600-1047600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
21	chr9:1046800-1047200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr9:1046800-1047400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr9:1046800-1047400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:1046800-1047600	Bivalent Enhancer	Brain Hippocampus Middle	brain
25	chr9:1046800-1047800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:1046800-1047800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr9:1046800-1047800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
28	chr9:1047000-1047200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:1047000-1047200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:1047000-1047200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
31	chr9:1047000-1047200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
32	chr9:1047000-1047400	Bivalent Enhancer	Liver	Liver
33	chr9:1047000-1047600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
34	chr9:1047000-1047600	Enhancers	Right Ventricle	heart
35	chr9:1047000-1047800	Enhancers	Lung	lung
36	chr9:1047000-1048000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
37	chr9:1047000-1048400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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