Variant report

Variant	rs12115728
Chromosome Location	chr9:116416276-116416277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116412180..116415022-chr9:116416036..116417817,2	MCF-7	breast:
2	chr9:116301103..116303347-chr9:116416136..116418556,2	MCF-7	breast:
3	chr9:116170045..116172847-chr9:116414698..116417875,3	MCF-7	breast:
4	chr9:116036759..116038980-chr9:116416097..116418826,3	MCF-7	breast:
5	chr9:116036462..116038120-chr9:116415759..116418139,2	K562	blood:
6	chr9:116342253..116346123-chr9:116415296..116418266,3	MCF-7	breast:
7	chr9:116412820..116415638-chr9:116416237..116418509,2	K562	blood:

Variant related genes	Relation type
ENSG00000227482	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10981864	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005477	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115627	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115685	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115730	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553649	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514603	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs680359	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73544656	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
4	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv466512	chr9:116413751-116446881	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv615220	chr9:116413751-116446881	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116411400-116416600	Weak transcription	Adipose Nuclei	Adipose
2	chr9:116411600-116420000	Weak transcription	Fetal Brain Female	brain
3	chr9:116411800-116417800	Enhancers	Liver	Liver
4	chr9:116412000-116416400	Weak transcription	Fetal Lung	lung
5	chr9:116412200-116417200	Weak transcription	Brain Anterior Caudate	brain
6	chr9:116412200-116417400	Weak transcription	Brain Angular Gyrus	brain
7	chr9:116412200-116417400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:116412200-116417600	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:116412400-116417200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:116412600-116417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:116412800-116416600	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:116412800-116420000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:116413200-116416600	Weak transcription	Spleen	Spleen
14	chr9:116413400-116416600	Weak transcription	Ovary	ovary
15	chr9:116413400-116416600	Weak transcription	NHLF	lung
16	chr9:116413400-116417200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:116413400-116417200	Weak transcription	NH-A	brain
18	chr9:116413400-116419000	Enhancers	HepG2	liver
19	chr9:116413400-116419800	Weak transcription	Fetal Kidney	kidney
20	chr9:116413400-116420000	Weak transcription	Gastric	stomach
21	chr9:116413600-116417400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:116413800-116416800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:116413800-116417000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:116413800-116417400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:116414000-116416600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:116414000-116417400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:116414000-116419400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:116414000-116420600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:116414200-116416800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:116414200-116417200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:116414200-116417400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr9:116414400-116417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:116414800-116417800	Enhancers	Fetal Heart	heart
34	chr9:116414800-116418200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr9:116415000-116417400	Enhancers	HUVEC	blood vessel
36	chr9:116415000-116418000	Enhancers	Right Atrium	heart
37	chr9:116415000-116418200	Enhancers	Right Ventricle	heart
38	chr9:116415200-116416400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:116415200-116416400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:116415200-116417200	Weak transcription	Fetal Intestine Large	intestine
41	chr9:116415200-116417400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:116415200-116417400	Weak transcription	NHEK	skin
43	chr9:116415400-116416600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:116415400-116416600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:116415400-116416600	Weak transcription	Fetal Intestine Small	intestine
46	chr9:116415400-116416600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:116415400-116416600	Weak transcription	HSMMtube	muscle
48	chr9:116415400-116416600	Weak transcription	NHDF-Ad	bronchial
49	chr9:116415400-116417000	Weak transcription	HSMM	muscle
50	chr9:116415400-116417000	Weak transcription	Osteobl	bone

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