Variant report

Variant	rs56280046
Chromosome Location	chr9:97862765-97862766
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97836720..97838496-chr9:97862659..97865053,2	MCF-7	breast:
2	chr9:97400366..97403518-chr9:97862496..97865550,3	MCF-7	breast:
3	chr9:97683938..97686249-chr9:97862761..97864573,2	MCF-7	breast:
4	chr7:155653017..155655598-chr9:97861454..97863217,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165140	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10453242	0.87[AFR][1000 genomes]
rs55651673	0.87[AFR][1000 genomes]
rs56025140	0.87[AFR][1000 genomes]
rs56134011	0.87[AFR][1000 genomes]
rs56737425	1.00[AFR][1000 genomes]
rs56761320	0.87[AFR][1000 genomes]
rs57312263	1.00[AFR][1000 genomes]
rs57883597	1.00[AFR][1000 genomes]
rs59611901	1.00[AFR][1000 genomes]
rs60346856	0.87[AFR][1000 genomes]
rs61462331	0.87[AFR][1000 genomes]
rs73654524	1.00[AFR][1000 genomes]
rs73654529	1.00[AFR][1000 genomes]
rs73654531	1.00[AFR][1000 genomes]
rs73654532	1.00[AFR][1000 genomes]
rs73654534	0.87[AFR][1000 genomes]
rs73654535	0.87[AFR][1000 genomes]
rs73654536	0.87[AFR][1000 genomes]
rs73654537	0.87[AFR][1000 genomes]
rs73654538	0.87[AFR][1000 genomes]
rs73654540	0.87[AFR][1000 genomes]
rs73654542	1.00[AFR][1000 genomes]
rs73654543	0.87[AFR][1000 genomes]
rs73654544	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
7	chr9:97847600-97878400	Weak transcription	Dnd41	blood
8	chr9:97849200-97863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:97849800-97864600	Enhancers	Psoas Muscle	Psoas
10	chr9:97855000-97867800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
12	chr9:97855400-97865400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:97855600-97862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:97855600-97863200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:97855600-97865400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
19	chr9:97856200-97872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:97856600-97865200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:97857400-97862800	Genic enhancers	A549	lung
22	chr9:97857800-97869600	Weak transcription	HUVEC	blood vessel
23	chr9:97858000-97862800	Weak transcription	Brain Anterior Caudate	brain
24	chr9:97858000-97863400	Strong transcription	Colonic Mucosa	Colon
25	chr9:97858000-97863800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:97858600-97863000	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:97858600-97867600	Genic enhancers	Fetal Muscle Leg	muscle
28	chr9:97858600-97877200	Strong transcription	Fetal Intestine Large	intestine
29	chr9:97858600-97878400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:97858800-97863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:97858800-97870800	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr9:97859000-97863200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:97859000-97865400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr9:97859200-97863400	Weak transcription	Brain Angular Gyrus	brain
35	chr9:97859200-97864200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:97859400-97863600	Weak transcription	Fetal Brain Male	brain
37	chr9:97859600-97865400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr9:97859800-97862800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr9:97860000-97875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:97860200-97867000	Enhancers	Fetal Heart	heart
41	chr9:97860400-97867800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:97860400-97879000	Strong transcription	Liver	Liver
43	chr9:97860600-97862800	Genic enhancers	Pancreas	Pancrea
44	chr9:97860600-97864800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:97860600-97865000	Enhancers	Esophagus	oesophagus
46	chr9:97860600-97865400	Genic enhancers	Placenta	Placenta
47	chr9:97860600-97869000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr9:97860600-97870200	Strong transcription	Thymus	Thymus
49	chr9:97860800-97863000	Genic enhancers	Gastric	stomach
50	chr9:97861000-97863600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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