Variant report

Variant	rs10115490
Chromosome Location	chr9:72004275-72004276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71996842..72001188-chr9:72001690..72005051,4	MCF-7	breast:
2	chr9:71734709..71737586-chr9:72003144..72005018,2	MCF-7	breast:
3	chr9:71937269..71941011-chr9:72000572..72004392,4	MCF-7	breast:
4	chr9:71905657..71909249-chr9:72003453..72006230,4	MCF-7	breast:
5	chr9:71991902..71994131-chr9:72003113..72004905,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10118562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746596	0.83[AFR][1000 genomes]
rs10780321	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10780324	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10780326	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10780336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867426	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10867436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11138304	0.91[ASN][1000 genomes]
rs11138332	0.91[ASN][1000 genomes]
rs11138334	0.91[ASN][1000 genomes]
rs11138402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11138412	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1334311	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829094	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3892193	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4112222	0.91[ASN][1000 genomes]
rs4421413	0.91[ASN][1000 genomes]
rs4458929	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4492445	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6559495	0.87[AFR][1000 genomes]
rs7047788	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7851643	0.91[ASN][1000 genomes]
rs7859544	0.91[ASN][1000 genomes]
rs7870082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
6	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:71994400-72006800	Weak transcription	Spleen	Spleen
8	chr9:71995000-72012600	Weak transcription	Aorta	Aorta
9	chr9:71997200-72005000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:71997200-72006600	Weak transcription	HSMMtube	muscle
11	chr9:71997400-72007400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:71997400-72009800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:71997600-72006200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:71997600-72006600	Weak transcription	Fetal Lung	lung
15	chr9:71998200-72005400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr9:72000000-72005000	Strong transcription	Ovary	ovary
17	chr9:72000200-72004800	Enhancers	Pancreas	Pancrea
18	chr9:72000200-72005000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:72000600-72006600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:72001000-72006600	Weak transcription	Lung	lung
21	chr9:72001600-72004400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:72001800-72006400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:72002200-72006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:72002400-72005200	Genic enhancers	Fetal Heart	heart
25	chr9:72002400-72006000	Weak transcription	Colon Smooth Muscle	Colon
26	chr9:72002400-72006400	Weak transcription	Right Ventricle	heart
27	chr9:72002400-72006800	Weak transcription	Gastric	stomach
28	chr9:72002600-72006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:72002800-72005000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr9:72002800-72012400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:72003200-72004400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:72003200-72005600	Weak transcription	Left Ventricle	heart
33	chr9:72003400-72004400	Weak transcription	Psoas Muscle	Psoas
34	chr9:72003400-72006000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:72003400-72006000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:72003400-72006400	Weak transcription	Adipose Nuclei	Adipose
37	chr9:72003400-72006400	Weak transcription	Brain Anterior Caudate	brain
38	chr9:72003400-72008400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:72003400-72010000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr9:72003400-72012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:72003400-72012400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:72003600-72005400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:72003600-72006200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:72003600-72006400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:72003600-72006400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr9:72003600-72006400	Weak transcription	Fetal Stomach	stomach
47	chr9:72003600-72026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr9:72003800-72006200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:72004000-72005000	Enhancers	Fetal Muscle Leg	muscle
50	chr9:72004200-72004800	Enhancers	Right Atrium	heart

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