Variant report

Variant	rs10780610
Chromosome Location	chr9:72366668-72366669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:72363859..72367648-chr9:72373327..72375290,5	MCF-7	breast:
2	chr9:72364400..72366683-chr9:72367530..72370078,2	MCF-7	breast:
3	chr9:72366292..72369666-chr9:72369993..72373484,7	K562	blood:
4	chr9:72360152..72362800-chr9:72364655..72369107,4	K562	blood:
5	chr9:72364587..72367878-chr9:72369030..72373518,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188647	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10118222	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119846	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217776	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735560	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10746706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746707	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780585	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867922	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868056	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11139996	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330238	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330240	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1330332	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411410	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1411413	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1536992	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536994	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547690	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1576482	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1576483	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1980934	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026794	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150045	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252130	0.96[ASN][1000 genomes]
rs2274745	1.00[ASN][1000 genomes]
rs2309531	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4535802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4535803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7023462	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7037769	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7039383	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851707	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7867543	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1048622	chr9:72303617-72371795	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72327800-72366800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:72333400-72374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:72347200-72371400	Weak transcription	Small Intestine	intestine
4	chr9:72347200-72373400	Weak transcription	Esophagus	oesophagus
5	chr9:72347200-72373400	Weak transcription	Fetal Intestine Small	intestine
6	chr9:72347200-72374200	Weak transcription	Spleen	Spleen
7	chr9:72347400-72374000	Weak transcription	Gastric	stomach
8	chr9:72347600-72368400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr9:72348800-72368600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:72348800-72373000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:72348800-72373000	Weak transcription	NHEK	skin
12	chr9:72348800-72373200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:72356800-72370000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:72359800-72373400	Weak transcription	Placenta	Placenta
15	chr9:72360000-72371400	Weak transcription	Pancreas	Pancrea
16	chr9:72360200-72372200	Weak transcription	HMEC	breast
17	chr9:72361200-72367400	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:72361400-72367000	Weak transcription	Stomach Mucosa	stomach
19	chr9:72361400-72371600	Weak transcription	K562	blood
20	chr9:72362400-72367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:72362400-72371400	Weak transcription	Right Atrium	heart
22	chr9:72362400-72373000	Weak transcription	Adipose Nuclei	Adipose
23	chr9:72362400-72373400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:72362600-72373200	Weak transcription	Fetal Stomach	stomach
25	chr9:72362800-72368800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:72362800-72373400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:72362800-72373400	Weak transcription	Aorta	Aorta
28	chr9:72363000-72368200	Weak transcription	HUVEC	blood vessel
29	chr9:72363000-72369400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr9:72363000-72373400	Weak transcription	Ovary	ovary
31	chr9:72363200-72367000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:72363200-72368600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr9:72363200-72373200	Weak transcription	Right Ventricle	heart
34	chr9:72363200-72374000	Weak transcription	Lung	lung
35	chr9:72363600-72371200	Weak transcription	Fetal Heart	heart
36	chr9:72363800-72370400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:72364000-72367400	Enhancers	Fetal Kidney	kidney
38	chr9:72364000-72373000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:72364200-72369400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
40	chr9:72364200-72372200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:72364200-72372400	Weak transcription	NH-A	brain
42	chr9:72364200-72373200	Weak transcription	HSMMtube	muscle
43	chr9:72364200-72373400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr9:72364400-72372200	Weak transcription	Osteobl	bone
45	chr9:72364400-72373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:72364600-72372400	Weak transcription	A549	lung
47	chr9:72364800-72370000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:72365000-72368000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr9:72365000-72368800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:72365000-72371600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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