Variant report

Variant	rs10116489
Chromosome Location	chr9:96792054-96792055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr9:96791934-96793709	U2OS	brain:	n/a	n/a
2	POLR2A	chr9:96791349-96793598	HepG2	liver:	n/a	n/a
3	HEY1	chr9:96791829-96792184	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:96791657-96792176	HepG2	liver:	n/a	n/a
5	MXI1	chr9:96791855-96794968	SK-N-SH	brain:	n/a	n/a
6	FOXA1	chr9:96791595-96792064	HepG2	liver:	n/a	n/a
7	POLR2A	chr9:96791930-96793346	K562	blood:	n/a	n/a
8	CEBPB	chr9:96792023-96792362	K562	blood:	n/a	n/a
9	FOXA1	chr9:96791712-96792097	HepG2	liver:	n/a	n/a
10	MAX	chr9:96791569-96792205	HepG2	liver:	n/a	n/a
11	TCF12	chr9:96792021-96793290	A549	lung:	n/a	chr9:96793212-96793222
12	POLR2A	chr9:96791749-96792219	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:96791676..96794493-chr9:96936767..96941836,4	MCF-7	breast:
2	chr9:96791956..96794354-chr9:96926207..96931491,6	MCF-7	breast:
3	chr9:96790378..96795979-chr9:96796527..96801819,13	MCF-7	breast:
4	chr9:96790823..96795467-chr9:96925835..96932235,7	K562	blood:
5	chr9:96791026..96792800-chr9:96856915..96858416,2	MCF-7	breast:
6	chr9:96789685..96792182-chr9:96794422..96796039,2	K562	blood:
7	chr9:96791196..96792768-chr9:96963356..96966651,3	MCF-7	breast:
8	chr9:96790406..96793524-chr9:96937356..96939962,3	MCF-7	breast:
9	chr9:96791020..96793870-chr9:96797908..96800825,2	K562	blood:
10	chr9:96790341..96794271-chr9:96926817..96931236,5	K562	blood:
11	chr9:96791853..96794356-chr9:96860367..96862558,2	MCF-7	breast:

No data

Variant related genes	Relation type
PTPDC1	TF binding region
ENSG00000199072	Chromatin interaction
ENSG00000227666	Chromatin interaction
ENSG00000269929	Chromatin interaction
ENSG00000199133	Chromatin interaction
ENSG00000158079	Chromatin interaction
ENSG00000269946	Chromatin interaction
ENSG00000199165	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10114421	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114811	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10116746	1.00[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];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10122071	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10125538	0.88[LWK][hapmap];0.85[YRI][hapmap]
rs10761314	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821272	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10821276	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821280	0.82[EUR][1000 genomes]
rs10821281	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10821283	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10821289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993003	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10993009	0.97[EUR][1000 genomes]
rs10993028	0.96[EUR][1000 genomes]
rs10993030	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10993032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993035	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993039	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]
rs10993044	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10993057	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11793324	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11795301	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12340234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12353106	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317246	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1592152	0.82[EUR][1000 genomes]
rs1819446	0.82[AFR][1000 genomes]
rs1854836	0.82[EUR][1000 genomes]
rs1933670	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1963282	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094929	0.82[EUR][1000 genomes]
rs2211361	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2225937	0.82[EUR][1000 genomes]
rs4743942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57094654	0.97[EUR][1000 genomes]
rs6479526	0.82[YRI][hapmap]
rs7020044	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7045483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7859394	0.81[EUR][1000 genomes]
rs7866395	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868385	0.82[EUR][1000 genomes]
rs932949	0.96[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv3426132	chr9:96782446-96794518	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96788600-96792200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:96788800-96792400	Weak transcription	Esophagus	oesophagus
3	chr9:96789000-96792400	Weak transcription	Pancreas	Pancrea
4	chr9:96789800-96792400	Weak transcription	Gastric	stomach
5	chr9:96789800-96792400	Weak transcription	Right Atrium	heart
6	chr9:96791800-96792200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:96791800-96792200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:96791800-96792200	Enhancers	Stomach Mucosa	stomach
9	chr9:96791800-96792200	Flanking Active TSS	A549	lung
10	chr9:96791800-96792200	Flanking Active TSS	HepG2	liver
11	chr9:96791800-96792400	Active TSS	Primary hematopoietic stem cells	blood
12	chr9:96791800-96792600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:96791800-96792600	Flanking Active TSS	Dnd41	blood
14	chr9:96791800-96793600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr9:96791800-96793800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr9:96791800-96794000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr9:96791800-96794200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:96792000-96792200	Enhancers	H9 Cell Line	embryonic stem cell
19	chr9:96792000-96792200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:96792000-96792200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr9:96792000-96792200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:96792000-96792200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:96792000-96792200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr9:96792000-96792200	Enhancers	Primary T cells from cord blood	blood
25	chr9:96792000-96792200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr9:96792000-96792200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr9:96792000-96792200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr9:96792000-96792200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:96792000-96792200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:96792000-96792200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:96792000-96792200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:96792000-96792200	Enhancers	Adipose Nuclei	Adipose
33	chr9:96792000-96792200	Enhancers	Colon Smooth Muscle	Colon
34	chr9:96792000-96792200	Enhancers	Fetal Muscle Leg	muscle
35	chr9:96792000-96792200	Enhancers	Fetal Stomach	stomach
36	chr9:96792000-96792200	Enhancers	Fetal Thymus	thymus
37	chr9:96792000-96792200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr9:96792000-96792200	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr9:96792000-96792200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr9:96792000-96792200	Enhancers	HUVEC	blood vessel
41	chr9:96792000-96792200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr9:96792000-96792200	Active TSS	NH-A	brain
43	chr9:96792000-96792200	Enhancers	NHDF-Ad	bronchial
44	chr9:96792000-96792200	Enhancers	NHEK	skin
45	chr9:96792000-96792200	Enhancers	Osteobl	bone
46	chr9:96792000-96792400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:96792000-96792400	Enhancers	Primary B cells from peripheral blood	blood
48	chr9:96792000-96792400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr9:96792000-96792400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:96792000-96792400	Active TSS	Stomach Smooth Muscle	stomach

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