Variant report

Variant	rs10993039
Chromosome Location	chr9:96827123-96827124
allele	C/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 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	chr9:96823995..96829172-chr9:96935840..96940267,7	K562	blood:
6	chr9:96823968..96833120-chr9:96926178..96930731,18	MCF-7	breast:
7	chr9:96790753..96794377-chr9:96825453..96830483,4	MCF-7	breast:
8	chr9:96826366..96828464-chr9:96974329..96976102,2	MCF-7	breast:

No data

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

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10114421	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10114811	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10116489	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10116746	0.94[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10122071	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10125538	0.93[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs10761314	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821272	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10821276	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.81[MKK][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821280	0.80[EUR][1000 genomes]
rs10821281	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10821283	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10821289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10993003	0.90[EUR][1000 genomes]
rs10993009	0.95[EUR][1000 genomes]
rs10993028	0.96[EUR][1000 genomes]
rs10993030	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10993035	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993044	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993057	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11793324	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11795301	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12340234	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12353106	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1317246	0.84[EUR][1000 genomes]
rs1592152	0.80[EUR][1000 genomes]
rs1854836	0.80[EUR][1000 genomes]
rs1933670	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1963282	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094929	0.80[EUR][1000 genomes]
rs2211361	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2225937	0.80[EUR][1000 genomes]
rs4743942	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57094654	0.95[EUR][1000 genomes]
rs6479526	0.91[MKK][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes]
rs7020044	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045483	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7859394	0.83[EUR][1000 genomes]
rs7866395	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7868385	0.80[EUR][1000 genomes]
rs932949	0.96[YRI][hapmap];0.80[AFR][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:43 , 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	chr9:96824400-96827200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:96824400-96828000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:96824400-96846600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:96824400-96850000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:96824600-96827200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:96824600-96827800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:96824600-96831200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:96824600-96832800	Weak transcription	Fetal Lung	lung
27	chr9:96824600-96836400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:96824600-96839400	Weak transcription	Left Ventricle	heart
29	chr9:96824600-96844400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:96824600-96845400	Weak transcription	Brain Germinal Matrix	brain
31	chr9:96824800-96829800	Weak transcription	Fetal Stomach	stomach
32	chr9:96824800-96832400	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:96824800-96832600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:96824800-96836400	Weak transcription	Fetal Intestine Small	intestine
35	chr9:96825000-96832400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:96825000-96836400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:96825200-96836600	Weak transcription	Lung	lung
38	chr9:96825200-96839800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:96825400-96832800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:96825400-96832800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:96826800-96827200	Enhancers	Ovary	ovary
42	chr9:96826800-96828000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr9:96827000-96827600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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