Variant report

Variant	rs1946750
Chromosome Location	chr12:66535021-66535022
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr12:66533659-66535801	K562	blood:	n/a	n/a
2	POLR2A	chr12:66532812-66535172	K562	blood:	n/a	n/a
3	KAP1	chr12:66533818-66535764	K562	blood:	n/a	n/a
4	SETDB1	chr12:66533904-66535566	U2OS	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66526618..66528298-chr12:66533657..66535201,2	MCF-7	breast:
2	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
3	chr12:66524217..66527472-chr12:66531631..66536698,7	K562	blood:
4	chr12:66522934..66525337-chr12:66532980..66535045,5	MCF-7	breast:
5	chr12:66531793..66533722-chr12:66534225..66536935,2	K562	blood:

No data

Variant related genes	Relation type
TMBIM4	TF binding region
ENSG00000155957	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10506476	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1058981	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176027	1.00[EUR][1000 genomes]
rs1152905	1.00[EUR][1000 genomes]
rs1152910	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1168738	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1168740	0.90[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1168741	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1168742	0.80[YRI][hapmap]
rs1168746	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1168756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1168764	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1168767	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1168773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1179916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1179917	0.82[YRI][hapmap]
rs12099497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1617632	1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102069	1.00[EUR][1000 genomes]
rs17102109	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102115	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1797400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1797401	1.00[AMR][1000 genomes]
rs6581665	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs7307987	1.00[EUR][1000 genomes]
rs7487759	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1946750	IRAK3	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:66525600-66536000	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:66525600-66536400	Weak transcription	Stomach Mucosa	stomach
4	chr12:66525600-66549000	Weak transcription	Colonic Mucosa	Colon
5	chr12:66525600-66552400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:66526400-66536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
9	chr12:66526800-66538600	Weak transcription	Hela-S3	cervix
10	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:66530000-66535400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:66530000-66535800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr12:66530000-66540800	Strong transcription	Placenta	Placenta
14	chr12:66530000-66544000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:66530000-66547200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:66530600-66536000	Strong transcription	HSMM	muscle
17	chr12:66530800-66535600	Weak transcription	NHLF	lung
18	chr12:66530800-66536000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:66531400-66537000	ZNF genes & repeats	GM12878-XiMat	blood
20	chr12:66531800-66535200	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:66532000-66536000	Weak transcription	HSMMtube	muscle
22	chr12:66532200-66536000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:66532400-66538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:66532600-66536400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:66532600-66536800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:66532600-66542600	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:66533000-66536000	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr12:66533000-66537000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:66533200-66536400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:66533200-66536400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:66533200-66536400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
32	chr12:66533200-66536400	ZNF genes & repeats	Fetal Lung	lung
33	chr12:66533200-66536600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:66533200-66536800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr12:66533200-66537200	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr12:66533200-66537400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr12:66533200-66537400	ZNF genes & repeats	Dnd41	blood
38	chr12:66533400-66535600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr12:66533400-66535600	Weak transcription	Osteobl	bone
40	chr12:66533400-66535800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:66533400-66536000	Strong transcription	NH-A	brain
42	chr12:66533400-66536400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr12:66533400-66536600	ZNF genes & repeats	HUVEC	blood vessel
44	chr12:66533400-66536600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
45	chr12:66533400-66537400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:66533600-66535600	ZNF genes & repeats	NHEK	skin
47	chr12:66533800-66535400	Weak transcription	Fetal Brain Male	brain
48	chr12:66533800-66535800	Weak transcription	Fetal Heart	heart
49	chr12:66533800-66536000	Weak transcription	Right Ventricle	heart
50	chr12:66533800-66536200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links