Variant report

Variant	rs12997263
Chromosome Location	chr2:11510487-11510488
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	MAX	chr2:11510413-11511459	HepG2	liver:	n/a	chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510830-11510843 chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510830-11510843
2	EP300	chr2:11510439-11511403	HepG2	liver:	n/a	n/a
3	MAX	chr2:11510476-11511230	MCF-7	breast:	n/a	chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510830-11510843 chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510830-11510843
4	TEAD4	chr2:11510211-11511466	HepG2	liver:	n/a	n/a
5	MAX	chr2:11510393-11511202	MCF-7	breast:	n/a	chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510830-11510843 chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510830-11510843
6	MAX	chr2:11510438-11512124	HepG2	liver:	n/a	chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510830-11510843 chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510830-11510843
7	MAX	chr2:11510422-11511742	A549	lung:	n/a	chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510830-11510843 chr2:11510812-11510823 chr2:11510832-11510841 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510830-11510843
8	MAFK	chr2:11510193-11510488	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11483340..11487694-chr2:11505828..11510815,5	K562	blood:
2	chr2:11494304..11496059-chr2:11510335..11513048,2	MCF-7	breast:
3	chr2:11483150..11486998-chr2:11509500..11514812,6	MCF-7	breast:
4	chr2:11483074..11486945-chr2:11508769..11511659,4	MCF-7	breast:
5	chr2:11506369..11508414-chr2:11509960..11513532,3	K562	blood:
6	chr2:11508308..11513224-chr2:11514143..11518077,7	MCF-7	breast:
7	chr2:11509703..11512447-chr2:11679988..11681680,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230952	TF binding region
ENSG00000134318	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12990641	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13015560	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13017021	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13020022	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34760292	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34887515	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35231136	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35665018	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35750432	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71439056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71439057	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12997263	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs12997263	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11505400-11514400	Enhancers	Fetal Intestine Large	intestine
2	chr2:11505600-11511600	Enhancers	Fetal Intestine Small	intestine
3	chr2:11505800-11511000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:11506000-11511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:11506000-11514600	Weak transcription	K562	blood
6	chr2:11506800-11511000	Enhancers	HepG2	liver
7	chr2:11507200-11511200	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:11507400-11516200	Enhancers	Stomach Mucosa	stomach
9	chr2:11508200-11510600	Weak transcription	Pancreas	Pancrea
10	chr2:11508400-11510600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:11508400-11510600	Weak transcription	Hela-S3	cervix
12	chr2:11508400-11513400	Weak transcription	HSMMtube	muscle
13	chr2:11508400-11514800	Weak transcription	Small Intestine	intestine
14	chr2:11508600-11513200	Weak transcription	NH-A	brain
15	chr2:11508600-11513600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:11508600-11514000	Enhancers	Psoas Muscle	Psoas
17	chr2:11508800-11510600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:11508800-11510800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:11508800-11510800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:11508800-11510800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:11508800-11511000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:11508800-11511000	Weak transcription	Fetal Lung	lung
23	chr2:11508800-11511000	Weak transcription	NHLF	lung
24	chr2:11508800-11513200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:11508800-11513400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:11508800-11513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:11508800-11513600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:11508800-11513600	Weak transcription	Osteobl	bone
29	chr2:11508800-11514400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:11508800-11514600	Weak transcription	Brain Germinal Matrix	brain
31	chr2:11508800-11514600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:11508800-11514600	Weak transcription	Right Atrium	heart
33	chr2:11508800-11515000	Weak transcription	Aorta	Aorta
34	chr2:11509000-11510600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:11509000-11510600	Weak transcription	NHDF-Ad	bronchial
36	chr2:11509000-11510800	Enhancers	Lung	lung
37	chr2:11509000-11513400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:11509000-11514400	Weak transcription	Brain Anterior Caudate	brain
39	chr2:11509000-11514400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:11509000-11514400	Weak transcription	Brain Substantia Nigra	brain
41	chr2:11509200-11510600	Weak transcription	Liver	Liver
42	chr2:11509200-11510800	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:11509200-11513200	Weak transcription	Left Ventricle	heart
44	chr2:11509200-11514400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:11509200-11514400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:11509400-11511000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:11509400-11511200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:11509400-11513600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:11509600-11511000	Weak transcription	Fetal Stomach	stomach
50	chr2:11509600-11512200	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links