Variant report

Variant	rs12005299
Chromosome Location	chr9:110006694-110006695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:110004629..110007184-chr9:110036620..110038464,2	MCF-7	breast:
2	chr9:110000595..110013733-chr9:110042800..110048700,27	MCF-7	breast:
3	chr9:110004582..110011651-chr9:110041707..110048879,25	MCF-7	breast:
4	chr9:109972512..109975127-chr9:110005713..110007836,2	MCF-7	breast:
5	chr9:109893618..109894481-chr9:110005806..110006859,6	MCF-7	breast:
6	chr9:109999870..110001713-chr9:110004205..110007979,4	K562	blood:
7	chr9:110005542..110008121-chr9:110058915..110061761,2	MCF-7	breast:
8	chr9:109893940..109894573-chr9:110005787..110006748,4	MCF-7	breast:
9	chr9:110006509..110008886-chr9:110028591..110031057,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10978789	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10978793	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11573631	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11573652	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11573655	0.93[EUR][1000 genomes]
rs11573700	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12001235	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001425	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12005522	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16912372	0.93[EUR][1000 genomes]
rs17724694	0.90[EUR][1000 genomes]
rs56091145	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567660	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567661	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567691	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567693	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567694	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62567696	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567704	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62567738	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73668766	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73668780	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7859324	0.94[EUR][1000 genomes];0.91[ASN][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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109998600-110006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:109999200-110008600	Weak transcription	Liver	Liver
3	chr9:110002000-110010000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:110002000-110011400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:110002400-110011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:110002400-110011200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:110002800-110010200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:110003400-110010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:110003600-110010800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:110004200-110008000	Weak transcription	Fetal Kidney	kidney
11	chr9:110004200-110011200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:110004800-110006800	Enhancers	Hela-S3	cervix
13	chr9:110004800-110007200	Enhancers	HMEC	breast
14	chr9:110004800-110007200	Enhancers	NHEK	skin
15	chr9:110005000-110007000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr9:110005400-110010000	Weak transcription	HSMMtube	muscle
17	chr9:110005600-110006800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr9:110005600-110006800	Enhancers	HepG2	liver
19	chr9:110006000-110007800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:110006000-110011000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:110006200-110007200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr9:110006200-110010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:110006400-110006800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:110006400-110008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:110006400-110008600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:110006400-110008600	Weak transcription	NHDF-Ad	bronchial
27	chr9:110006400-110008800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:110006400-110010000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:110006400-110010000	Weak transcription	Psoas Muscle	Psoas
30	chr9:110006400-110010200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:110006400-110010400	Weak transcription	HSMM	muscle
32	chr9:110006400-110011000	Weak transcription	NHLF	lung
33	chr9:110006400-110011000	Weak transcription	Osteobl	bone
34	chr9:110006400-110011200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:110006400-110011200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr9:110006600-110008600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:110006600-110008600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:110006600-110008800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:110006600-110008800	Weak transcription	A549	lung
40	chr9:110006600-110008800	Weak transcription	GM12878-XiMat	blood
41	chr9:110006600-110009800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:110006600-110010200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr9:110006600-110010400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:110006600-110013000	Enhancers	Placenta	Placenta
45	chr9:110006600-110013600	Weak transcription	NH-A	brain

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