Variant report

Variant	rs13020022
Chromosome Location	chr2:11510605-11510606
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	TCF12	chr2:11510524-11511552	A549	lung:	n/a	chr2:11511010-11511018
2	NR2F2	chr2:11510509-11511376	MCF-7	breast:	n/a	n/a
3	SP1	chr2:11510519-11511312	HepG2	liver:	n/a	n/a
4	EP300	chr2:11510595-11511214	HepG2	liver:	n/a	n/a
5	TCF12	chr2:11510592-11511173	HepG2	liver:	n/a	chr2:11511010-11511018
6	GATA3	chr2:11510541-11511301	MCF-7	breast:	n/a	n/a
7	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
8	ELF1	chr2:11510605-11511157	HepG2	liver:	n/a	n/a
9	USF1	chr2:11510581-11511107	SK-N-SH	brain:	n/a	chr2:11510826-11510847 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510832-11510841 chr2:11510833-11510842 chr2:11510813-11510822 chr2:11510831-11510840 chr2:11510830-11510841 chr2:11510830-11510843
10	NFIC	chr2:11510577-11511200	HepG2	liver:	n/a	n/a
11	MBD4	chr2:11510519-11511396	HepG2	liver:	n/a	n/a
12	EP300	chr2:11510439-11511403	HepG2	liver:	n/a	n/a
13	FOXA2	chr2:11510592-11511328	HepG2	liver:	n/a	n/a
14	MAX	chr2:11510604-11511047	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
15	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
16	SP1	chr2:11510577-11511271	A549	lung:	n/a	n/a
17	HDAC2	chr2:11510561-11511329	HepG2	liver:	n/a	n/a
18	HNF4G	chr2:11510598-11511263	HepG2	liver:	n/a	chr2:11511039-11511046 chr2:11511035-11511051
19	MAX	chr2:11510525-11511222	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
20	REST	chr2:11510604-11511169	HepG2	liver:	n/a	n/a
21	TEAD4	chr2:11510211-11511466	HepG2	liver:	n/a	n/a
22	NR2F2	chr2:11510527-11511442	MCF-7	breast:	n/a	n/a
23	MYBL2	chr2:11510530-11511643	HepG2	liver:	n/a	n/a
24	HDAC2	chr2:11510597-11511316	HepG2	liver:	n/a	n/a
25	HNF4A	chr2:11510594-11511281	HepG2	liver:	n/a	chr2:11511039-11511046 chr2:11511035-11511051
26	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
27	MBD4	chr2:11510502-11511571	HepG2	liver:	n/a	n/a
28	MYBL2	chr2:11510575-11511408	HepG2	liver:	n/a	n/a
29	BHLHE40	chr2:11510585-11511130	HepG2	liver:	n/a	chr2:11510826-11510847 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510832-11510841 chr2:11510833-11510842 chr2:11510813-11510822 chr2:11510831-11510840 chr2:11510830-11510843
30	NFIC	chr2:11510499-11511562	HepG2	liver:	n/a	n/a
31	HNF4A	chr2:11510557-11511277	HepG2	liver:	n/a	chr2:11511039-11511046 chr2:11511035-11511051
32	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
33	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
34	USF1	chr2:11510568-11511050	ECC-1	luminal epithelium:	n/a	chr2:11510826-11510847 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510832-11510841 chr2:11510833-11510842 chr2:11510813-11510822 chr2:11510831-11510840 chr2:11510830-11510841 chr2:11510830-11510843
35	BHLHE40	chr2:11510529-11511488	HepG2	liver:	n/a	chr2:11510826-11510847 chr2:11510832-11510841 chr2:11510813-11510822 chr2:11510832-11510841 chr2:11510833-11510842 chr2:11510813-11510822 chr2:11510831-11510840 chr2:11510830-11510843
36	RXRA	chr2:11510548-11511201	HepG2	liver:	n/a	chr2:11511133-11511149

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	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12997263	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13015560	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13017021	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34760292	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34887515	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35231136	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35665018	0.93[EUR][1000 genomes]
rs35750432	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71439056	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71439057	0.97[AMR][1000 genomes];0.97[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
rs13020022	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs13020022	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 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	chr2:11508400-11513400	Weak transcription	HSMMtube	muscle
10	chr2:11508400-11514800	Weak transcription	Small Intestine	intestine
11	chr2:11508600-11513200	Weak transcription	NH-A	brain
12	chr2:11508600-11513600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:11508600-11514000	Enhancers	Psoas Muscle	Psoas
14	chr2:11508800-11510800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:11508800-11510800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:11508800-11510800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr2:11508800-11511000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:11508800-11511000	Weak transcription	Fetal Lung	lung
19	chr2:11508800-11511000	Weak transcription	NHLF	lung
20	chr2:11508800-11513200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:11508800-11513400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:11508800-11513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:11508800-11513600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:11508800-11513600	Weak transcription	Osteobl	bone
25	chr2:11508800-11514400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:11508800-11514600	Weak transcription	Brain Germinal Matrix	brain
27	chr2:11508800-11514600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:11508800-11514600	Weak transcription	Right Atrium	heart
29	chr2:11508800-11515000	Weak transcription	Aorta	Aorta
30	chr2:11509000-11510800	Enhancers	Lung	lung
31	chr2:11509000-11513400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:11509000-11514400	Weak transcription	Brain Anterior Caudate	brain
33	chr2:11509000-11514400	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:11509000-11514400	Weak transcription	Brain Substantia Nigra	brain
35	chr2:11509200-11510800	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:11509200-11513200	Weak transcription	Left Ventricle	heart
37	chr2:11509200-11514400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:11509200-11514400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:11509400-11511000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:11509400-11511200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr2:11509400-11513600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:11509600-11511000	Weak transcription	Fetal Stomach	stomach
43	chr2:11509600-11512200	Enhancers	Colonic Mucosa	Colon
44	chr2:11509600-11513400	Weak transcription	Adipose Nuclei	Adipose
45	chr2:11509600-11513600	Enhancers	Gastric	stomach
46	chr2:11509600-11513800	Weak transcription	Placenta	Placenta
47	chr2:11509800-11512200	Enhancers	A549	lung
48	chr2:11509800-11512400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:11509800-11512800	Weak transcription	Spleen	Spleen
50	chr2:11509800-11513800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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