Variant report

Variant	rs12235653
Chromosome Location	chr9:86615786-86615787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86612231..86616038-chr9:86617136..86619825,3	K562	blood:
2	chr9:86611159..86613982-chr9:86615279..86618286,3	MCF-7	breast:
3	chr9:86591784..86594593-chr9:86615080..86617592,2	MCF-7	breast:
4	chr9:86599801..86602585-chr9:86615309..86617946,2	K562	blood:

Variant related genes	Relation type
ENSG00000165119	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10780645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10868067	0.93[EUR][1000 genomes]
rs11140269	0.85[EUR][1000 genomes]
rs11140270	0.85[EUR][1000 genomes]
rs11140271	1.00[EUR][1000 genomes]
rs11140274	0.92[EUR][1000 genomes]
rs11140275	0.92[EUR][1000 genomes]
rs11140280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140288	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140290	0.86[EUR][1000 genomes]
rs11140291	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11140292	1.00[EUR][1000 genomes]
rs11140294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140296	1.00[EUR][1000 genomes]
rs11140308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140309	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140312	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140313	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140318	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140321	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140322	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140337	1.00[EUR][1000 genomes]
rs11140338	1.00[EUR][1000 genomes]
rs11531847	1.00[EUR][1000 genomes]
rs11533022	1.00[EUR][1000 genomes]
rs11533047	0.93[EUR][1000 genomes]
rs11535577	1.00[EUR][1000 genomes]
rs11559387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs12056961	1.00[EUR][1000 genomes]
rs12235969	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12237056	1.00[EUR][1000 genomes]
rs12237297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017558	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59409125	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60989495	0.86[EUR][1000 genomes]
rs73471357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9776332	0.93[EUR][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	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv3328820	chr9:86613612-86634313	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
2	chr9:86596600-86616000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:86596600-86617000	Weak transcription	Lung	lung
4	chr9:86596600-86618200	Weak transcription	Ovary	ovary
5	chr9:86596600-86619600	Weak transcription	Gastric	stomach
6	chr9:86596800-86616000	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:86596800-86616200	Weak transcription	Brain Angular Gyrus	brain
8	chr9:86596800-86616200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr9:86596800-86619600	Weak transcription	Small Intestine	intestine
10	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:86597000-86616000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:86597000-86616000	Weak transcription	Fetal Lung	lung
14	chr9:86597000-86617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:86597000-86621200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:86597000-86621600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:86597200-86616000	Weak transcription	Fetal Kidney	kidney
18	chr9:86597200-86616800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr9:86597200-86619000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:86597400-86628800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:86597600-86615800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:86598000-86615800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:86598800-86622400	Weak transcription	Brain Germinal Matrix	brain
24	chr9:86602000-86616000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:86602000-86616000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:86602000-86620800	Weak transcription	NHLF	lung
27	chr9:86602000-86623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:86602200-86616000	Weak transcription	HSMM	muscle
29	chr9:86602200-86617400	Weak transcription	Osteobl	bone
30	chr9:86602200-86618000	Weak transcription	NHEK	skin
31	chr9:86602200-86618200	Weak transcription	Placenta	Placenta
32	chr9:86602400-86616000	Weak transcription	Primary B cells from cord blood	blood
33	chr9:86602400-86616000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:86602400-86616200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:86602400-86618000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:86602400-86627200	Weak transcription	Left Ventricle	heart
37	chr9:86602600-86620000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr9:86602800-86617400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr9:86603600-86619600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:86603800-86621200	Weak transcription	Hela-S3	cervix
41	chr9:86604000-86622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:86604000-86626200	Weak transcription	Pancreas	Pancrea
43	chr9:86604200-86618200	Weak transcription	HMEC	breast
44	chr9:86604200-86621400	Weak transcription	Thymus	Thymus
45	chr9:86604200-86623400	Weak transcription	Fetal Stomach	stomach
46	chr9:86604400-86616200	Weak transcription	Fetal Brain Female	brain
47	chr9:86605000-86616000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:86605000-86622400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:86605200-86616000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:86605200-86620600	Weak transcription	Rectal Mucosa Donor 29	rectum

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