Variant report

Variant	rs2298490
Chromosome Location	chr11:113233059-113233060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:113232995-113233211	HepG2	liver:	n/a	chr11:113233071-113233082 chr11:113233071-113233082 chr11:113233072-113233083 chr11:113233072-113233083 chr11:113233070-113233084
2	MAFK	chr11:113233027-113233171	HepG2	liver:	n/a	chr11:113233071-113233082 chr11:113233071-113233082 chr11:113233072-113233083 chr11:113233072-113233083 chr11:113233070-113233084

Variant related genes	Relation type
TTC12	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1055075	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10891543	0.88[ASN][1000 genomes]
rs10891546	0.95[JPT][hapmap]
rs11214579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12282356	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17115439	0.95[JPT][hapmap]
rs1893696	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2155464	0.86[ASN][1000 genomes]
rs2276070	0.82[CHB][hapmap]
rs2282511	0.86[ASN][1000 genomes]
rs2298489	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2303380	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3897584	0.88[ASN][1000 genomes]
rs4601821	0.88[ASN][1000 genomes]
rs4938012	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4938013	0.95[JPT][hapmap]
rs4938015	0.95[JPT][hapmap]
rs6589375	0.86[ASN][1000 genomes]
rs7114433	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7115082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118900	0.81[JPT][hapmap]
rs7123797	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7130431	0.85[ASN][1000 genomes]
rs713233	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs719802	0.84[CEU][hapmap]
rs719803	0.82[CHB][hapmap]
rs7945132	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs877138	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2298490	TTC12	cis	Heart Left Ventricle	GTEx
rs2298490	TTC12	cis	Thyroid	GTEx
rs2298490	TTC12	cis	Esophagus Muscularis	GTEx
rs2298490	TTC12	cis	lung	GTEx
rs2298490	TTC12	cis	Muscle Skeletal	GTEx
rs2298490	TTC12	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113186800-113234200	Weak transcription	Fetal Thymus	thymus
2	chr11:113195600-113240600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:113203200-113248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:113204000-113240600	Weak transcription	Stomach Mucosa	stomach
5	chr11:113208600-113239000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:113208800-113238200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:113210600-113243600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:113210800-113234600	Weak transcription	A549	lung
9	chr11:113210800-113235000	Weak transcription	Thymus	Thymus
10	chr11:113213000-113243000	Weak transcription	NHLF	lung
11	chr11:113215400-113243600	Weak transcription	Osteobl	bone
12	chr11:113218400-113233400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:113220400-113236200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:113220800-113233600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:113222600-113238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:113225000-113233600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:113226400-113233800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:113226600-113242400	Strong transcription	Stomach Smooth Muscle	stomach
19	chr11:113227000-113238600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:113227000-113239400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr11:113227200-113235600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:113227200-113236400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:113227400-113233400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:113227400-113233800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:113227400-113233800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:113227400-113235600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:113227400-113236400	Weak transcription	Primary T cells from cord blood	blood
28	chr11:113227400-113236600	Strong transcription	Ovary	ovary
29	chr11:113227400-113239800	Strong transcription	Liver	Liver
30	chr11:113227400-113241200	Weak transcription	Psoas Muscle	Psoas
31	chr11:113227600-113235800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:113227600-113237200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr11:113227800-113241000	Strong transcription	Adipose Nuclei	Adipose
34	chr11:113228000-113239400	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:113228200-113237600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr11:113228200-113239600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr11:113228400-113236400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:113228400-113238200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:113228400-113239400	Strong transcription	Left Ventricle	heart
40	chr11:113228400-113239600	Strong transcription	Fetal Muscle Leg	muscle
41	chr11:113228400-113240200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr11:113228400-113240800	Strong transcription	Fetal Intestine Large	intestine
43	chr11:113228600-113239400	Strong transcription	Aorta	Aorta
44	chr11:113228600-113241600	Strong transcription	Fetal Intestine Small	intestine
45	chr11:113229000-113233800	Weak transcription	GM12878-XiMat	blood
46	chr11:113229000-113239400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:113229200-113233800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:113229200-113240400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:113229200-113246800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr11:113229400-113237000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links