Variant report

Variant	rs713233
Chromosome Location	chr11:113234466-113234467
allele	A/G
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	STAT3	chr11:113234400-113234540	MCF10A-Er-Src	breast:	n/a	n/a
2	RUNX3	chr11:113234238-113234708	GM12878	blood:	n/a	chr11:113234483-113234498
3	NR3C1	chr11:113234271-113234494	ECC-1	luminal epithelium:	n/a	chr11:113234411-113234427 chr11:113234370-113234384 chr11:113234411-113234427 chr11:113234412-113234426 chr11:113234412-113234426 chr11:113234411-113234427
4	NR3C1	chr11:113234146-113234518	A549	lung:	n/a	chr11:113234411-113234427 chr11:113234370-113234384 chr11:113234411-113234427 chr11:113234412-113234426 chr11:113234412-113234426 chr11:113234411-113234427
5	RUNX3	chr11:113234216-113234736	GM12878	blood:	n/a	chr11:113234483-113234498
6	NR3C1	chr11:113234140-113234563	A549	lung:	n/a	chr11:113234411-113234427 chr11:113234370-113234384 chr11:113234411-113234427 chr11:113234412-113234426 chr11:113234412-113234426 chr11:113234411-113234427

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:113234115..113236597-chr11:113236900..113239444,2	K562	blood:

Variant related genes	Relation type
ENSG00000270179	TF binding region
TTC12	TF binding region
ENSG00000270179	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10502173	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1055076	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10891541	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10891542	0.83[ASN][1000 genomes]
rs10891545	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1124492	0.85[JPT][hapmap]
rs12224538	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs12225351	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12285457	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12292113	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12293753	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1943622	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2187346	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2276070	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288159	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298489	0.81[YRI][hapmap]
rs2298490	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2859545	0.85[JPT][hapmap]
rs28712705	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3781884	0.81[CHB][hapmap]
rs4590907	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs4938007	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4938010	0.89[EUR][1000 genomes]
rs4938011	0.86[EUR][1000 genomes]
rs4938014	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs4987094	0.80[CHB][hapmap]
rs6589372	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6589373	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7109196	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7115082	0.81[ASN][1000 genomes]
rs719803	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7928201	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928978	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7931066	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7949242	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs948176	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs713233	TTC12	cis	multi-tissue	Pritchard
rs713233	TTC12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113195600-113240600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:113203200-113248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:113204000-113240600	Weak transcription	Stomach Mucosa	stomach
4	chr11:113208600-113239000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:113208800-113238200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:113210600-113243600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:113210800-113234600	Weak transcription	A549	lung
8	chr11:113210800-113235000	Weak transcription	Thymus	Thymus
9	chr11:113213000-113243000	Weak transcription	NHLF	lung
10	chr11:113215400-113243600	Weak transcription	Osteobl	bone
11	chr11:113220400-113236200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:113222600-113238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:113226600-113242400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr11:113227000-113238600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:113227000-113239400	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr11:113227200-113235600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:113227200-113236400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:113227400-113235600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:113227400-113236400	Weak transcription	Primary T cells from cord blood	blood
20	chr11:113227400-113236600	Strong transcription	Ovary	ovary
21	chr11:113227400-113239800	Strong transcription	Liver	Liver
22	chr11:113227400-113241200	Weak transcription	Psoas Muscle	Psoas
23	chr11:113227600-113235800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr11:113227600-113237200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr11:113227800-113241000	Strong transcription	Adipose Nuclei	Adipose
26	chr11:113228000-113239400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:113228200-113237600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr11:113228200-113239600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr11:113228400-113236400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:113228400-113238200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:113228400-113239400	Strong transcription	Left Ventricle	heart
32	chr11:113228400-113239600	Strong transcription	Fetal Muscle Leg	muscle
33	chr11:113228400-113240200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr11:113228400-113240800	Strong transcription	Fetal Intestine Large	intestine
35	chr11:113228600-113239400	Strong transcription	Aorta	Aorta
36	chr11:113228600-113241600	Strong transcription	Fetal Intestine Small	intestine
37	chr11:113229000-113239400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:113229200-113240400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:113229200-113246800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr11:113229400-113237000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:113229400-113246600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:113229800-113243800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:113230200-113238400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:113230200-113239800	Weak transcription	Primary B cells from cord blood	blood
45	chr11:113230400-113236400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr11:113230400-113241000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:113230400-113243800	Weak transcription	HSMMtube	muscle
48	chr11:113230600-113234600	Weak transcription	Placenta	Placenta
49	chr11:113230600-113246400	Weak transcription	Fetal Heart	heart
50	chr11:113231800-113246000	Weak transcription	Fetal Brain Male	brain

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