Variant report

Variant	rs12685502
Chromosome Location	chr9:100856447-100856448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100854857..100858216-chr9:100859815..100862385,4	K562	blood:
2	chr9:100855944..100858108-chr9:100861699..100863538,2	MCF-7	breast:
3	chr9:100849256..100851636-chr9:100854662..100858526,4	MCF-7	breast:
4	chr9:100855541..100857442-chr9:101017373..101019341,2	MCF-7	breast:
5	chr9:100849838..100852817-chr9:100854861..100857855,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095383	Chromatin interaction
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10124238	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1058446	0.81[AMR][1000 genomes]
rs10818454	0.84[CHD][hapmap]
rs10818468	0.87[CHD][hapmap];0.81[AMR][1000 genomes]
rs10818472	0.91[CHD][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes]
rs10984977	0.84[AMR][1000 genomes]
rs12348197	0.83[AMR][1000 genomes]
rs16912590	0.91[CHD][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs28489815	0.81[AMR][1000 genomes]
rs7037233	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9969738	0.81[AMR][1000 genomes]
rs9969813	0.94[CHD][hapmap];0.81[AMR][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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040483	chr9:100835325-100868437	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12685502	TBC1D2	cis	lymphoblastoid	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100839400-100861800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr9:100845200-100856600	Weak transcription	Small Intestine	intestine
3	chr9:100846000-100862600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:100846200-100862200	Strong transcription	Duodenum Mucosa	Duodenum
5	chr9:100846400-100861200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:100847400-100859400	Weak transcription	HepG2	liver
7	chr9:100847400-100869400	Weak transcription	A549	lung
8	chr9:100847600-100867000	Weak transcription	Hela-S3	cervix
9	chr9:100850400-100856600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:100850400-100856600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:100850400-100856600	Weak transcription	Esophagus	oesophagus
12	chr9:100850400-100856600	Weak transcription	Gastric	stomach
13	chr9:100850400-100856600	Weak transcription	Stomach Mucosa	stomach
14	chr9:100850400-100856800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:100850400-100857800	Weak transcription	Aorta	Aorta
16	chr9:100850400-100858000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:100850400-100859000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:100850400-100861000	Weak transcription	HMEC	breast
19	chr9:100850400-100868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:100850400-100880400	Weak transcription	HSMM	muscle
21	chr9:100850600-100856600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:100850600-100856800	Weak transcription	Brain Anterior Caudate	brain
23	chr9:100850600-100857200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:100850600-100858000	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:100850600-100863000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr9:100850600-100864400	Weak transcription	Brain Germinal Matrix	brain
27	chr9:100850600-100875400	Weak transcription	NHLF	lung
28	chr9:100850600-100880600	Weak transcription	Fetal Lung	lung
29	chr9:100850800-100857000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr9:100850800-100858600	Weak transcription	Primary B cells from cord blood	blood
31	chr9:100850800-100859000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr9:100851000-100862800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr9:100851400-100859600	Strong transcription	Fetal Intestine Small	intestine
34	chr9:100851400-100861200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:100851600-100859800	Strong transcription	Primary T cells from cord blood	blood
36	chr9:100851800-100860200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:100852000-100859000	Weak transcription	GM12878-XiMat	blood
38	chr9:100852000-100861600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:100852800-100858800	Weak transcription	K562	blood
40	chr9:100853000-100862400	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr9:100853200-100862000	Strong transcription	Dnd41	blood
42	chr9:100853400-100861800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr9:100853600-100861800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr9:100854400-100862000	Strong transcription	Fetal Intestine Large	intestine
45	chr9:100854600-100859800	Weak transcription	HSMMtube	muscle
46	chr9:100854600-100860400	Weak transcription	Fetal Brain Female	brain
47	chr9:100854600-100870800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:100854800-100857400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:100854800-100858600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:100854800-100859400	Strong transcription	Lung	lung

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