Variant report

Variant	rs1539282
Chromosome Location	chr9:96827424-96827425
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96822397..96829591-chr9:96927085..96931647,12	MCF-7	breast:
2	chr9:96820485..96823456-chr9:96825806..96827839,3	MCF-7	breast:
3	chr9:96824401..96829621-chr9:96935642..96938972,5	K562	blood:
4	chr9:96825007..96827841-chr9:96858083..96859846,2	K562	blood:
5	chr9:96827200..96828396-chr9:96975283..96976482,6	MCF-7	breast:
6	chr9:96827423..96828438-chr9:96975497..96976368,7	K562	blood:
7	chr9:96823995..96829172-chr9:96935840..96940267,7	K562	blood:
8	chr9:96823968..96833120-chr9:96926178..96930731,18	MCF-7	breast:
9	chr9:96827369..96828051-chr9:96923205..96923887,3	MCF-7	breast:
10	chr9:96790753..96794377-chr9:96825453..96830483,4	MCF-7	breast:
11	chr9:96826366..96828464-chr9:96974329..96976102,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158079	Chromatin interaction
ENSG00000199165	Chromatin interaction
ENSG00000269929	Chromatin interaction
ENSG00000199072	Chromatin interaction
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10993017	0.87[CEU][hapmap]
rs10993047	0.88[CEU][hapmap]
rs11788176	0.96[CEU][hapmap]
rs11789015	0.83[CEU][hapmap]
rs11789837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791859	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11793856	0.86[CEU][hapmap]
rs11999153	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004383	0.90[CEU][hapmap]
rs12684081	0.88[CEU][hapmap]
rs1411861	0.96[CEU][hapmap]
rs2039313	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34169833	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4319160	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514041	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047684	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7855830	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870790	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7872984	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
3	nsv1043704	chr9:96816552-96873018	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96794200-96828000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:96819000-96833400	Weak transcription	HSMM	muscle
3	chr9:96819400-96828000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:96819400-96832800	Weak transcription	HSMMtube	muscle
5	chr9:96819600-96827600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:96819600-96828000	Weak transcription	NHDF-Ad	bronchial
7	chr9:96820600-96836400	Weak transcription	Pancreas	Pancrea
8	chr9:96822400-96859800	Weak transcription	Psoas Muscle	Psoas
9	chr9:96822600-96832800	Weak transcription	Primary T cells from cord blood	blood
10	chr9:96824000-96845000	Weak transcription	Right Ventricle	heart
11	chr9:96824200-96827600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:96824200-96827600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:96824200-96828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:96824200-96829200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:96824200-96832800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:96824200-96836600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:96824200-96860000	Weak transcription	Aorta	Aorta
18	chr9:96824200-96869600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr9:96824400-96828000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:96824400-96846600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:96824400-96850000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:96824600-96827800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:96824600-96831200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:96824600-96832800	Weak transcription	Fetal Lung	lung
25	chr9:96824600-96836400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:96824600-96839400	Weak transcription	Left Ventricle	heart
27	chr9:96824600-96844400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:96824600-96845400	Weak transcription	Brain Germinal Matrix	brain
29	chr9:96824800-96829800	Weak transcription	Fetal Stomach	stomach
30	chr9:96824800-96832400	Weak transcription	Fetal Muscle Leg	muscle
31	chr9:96824800-96832600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:96824800-96836400	Weak transcription	Fetal Intestine Small	intestine
33	chr9:96825000-96832400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:96825000-96836400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:96825200-96836600	Weak transcription	Lung	lung
36	chr9:96825200-96839800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:96825400-96832800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:96825400-96832800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:96826800-96828000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr9:96827000-96827600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:96827200-96828400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:96827200-96828400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:96827400-96827800	Genic enhancers	Ovary	ovary
44	chr9:96827400-96828000	Weak transcription	Fetal Intestine Large	intestine
45	chr9:96827400-96828200	Enhancers	Adipose Nuclei	Adipose
46	chr9:96827400-96828200	Enhancers	Brain Cingulate Gyrus	brain
47	chr9:96827400-96828200	Enhancers	Right Atrium	heart
48	chr9:96827400-96828400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr9:96827400-96828400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr9:96827400-96828600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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