Variant report

Variant	rs13015560
Chromosome Location	chr2:11511919-11511920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11494304..11496059-chr2:11510335..11513048,2	MCF-7	breast:
2	chr2:11483150..11486998-chr2:11509500..11514812,6	MCF-7	breast:
3	chr2:11511258..11513746-chr2:11518723..11520473,2	MCF-7	breast:
4	chr2:11506369..11508414-chr2:11509960..11513532,3	K562	blood:
5	chr2:11508308..11513224-chr2:11514143..11518077,7	MCF-7	breast:
6	chr2:11511350..11513048-chr2:11514615..11516700,2	K562	blood:
7	chr2:11511588..11513263-chr2:11524168..11525755,2	MCF-7	breast:
8	chr2:11509703..11512447-chr2:11679988..11681680,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10194620	0.80[CEU][hapmap]
rs10203916	0.87[CEU][hapmap]
rs10205944	0.87[CEU][hapmap]
rs10210600	0.81[CEU][hapmap]
rs10454126	0.83[CEU][hapmap]
rs11694729	0.87[CEU][hapmap]
rs11695377	0.83[CEU][hapmap]
rs12692434	0.82[CEU][hapmap]
rs12692437	0.86[CEU][hapmap]
rs12990641	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12997263	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13017021	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13020022	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1562748	0.83[CEU][hapmap]
rs1562749	0.88[CEU][hapmap]
rs1868584	0.88[CEU][hapmap]
rs2044758	0.88[CEU][hapmap]
rs2084577	0.83[CEU][hapmap]
rs2357996	0.87[CEU][hapmap]
rs34760292	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34887515	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35231136	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35665018	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35750432	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3911110	0.83[CEU][hapmap]
rs4669710	0.83[CEU][hapmap]
rs4669713	0.83[CEU][hapmap]
rs4669715	0.93[CEU][hapmap]
rs6432183	0.88[CEU][hapmap]
rs6432184	0.88[CEU][hapmap]
rs6432186	0.83[CEU][hapmap]
rs6713273	0.87[CEU][hapmap]
rs6721445	0.83[CEU][hapmap]
rs6733312	0.82[CEU][hapmap]
rs6749456	0.87[CEU][hapmap]
rs6755196	0.83[CEU][hapmap]
rs6760802	0.93[CEU][hapmap]
rs71439056	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71439057	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71439058	0.84[EUR][1000 genomes]
rs7355446	0.82[CEU][hapmap]
rs753770	0.87[CEU][hapmap]
rs7563928	0.82[CEU][hapmap]
rs7593091	0.87[CEU][hapmap]
rs9287728	0.88[CEU][hapmap]
rs965665	0.88[CEU][hapmap]

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
rs13015560	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs13015560	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11505400-11514400	Enhancers	Fetal Intestine Large	intestine
2	chr2:11506000-11514600	Weak transcription	K562	blood
3	chr2:11507400-11516200	Enhancers	Stomach Mucosa	stomach
4	chr2:11508400-11513400	Weak transcription	HSMMtube	muscle
5	chr2:11508400-11514800	Weak transcription	Small Intestine	intestine
6	chr2:11508600-11513200	Weak transcription	NH-A	brain
7	chr2:11508600-11513600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:11508600-11514000	Enhancers	Psoas Muscle	Psoas
9	chr2:11508800-11513200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:11508800-11513400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:11508800-11513600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:11508800-11513600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:11508800-11513600	Weak transcription	Osteobl	bone
14	chr2:11508800-11514400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:11508800-11514600	Weak transcription	Brain Germinal Matrix	brain
16	chr2:11508800-11514600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:11508800-11514600	Weak transcription	Right Atrium	heart
18	chr2:11508800-11515000	Weak transcription	Aorta	Aorta
19	chr2:11509000-11513400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:11509000-11514400	Weak transcription	Brain Anterior Caudate	brain
21	chr2:11509000-11514400	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:11509000-11514400	Weak transcription	Brain Substantia Nigra	brain
23	chr2:11509200-11513200	Weak transcription	Left Ventricle	heart
24	chr2:11509200-11514400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:11509200-11514400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:11509400-11513600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:11509600-11512200	Enhancers	Colonic Mucosa	Colon
28	chr2:11509600-11513400	Weak transcription	Adipose Nuclei	Adipose
29	chr2:11509600-11513600	Enhancers	Gastric	stomach
30	chr2:11509600-11513800	Weak transcription	Placenta	Placenta
31	chr2:11509800-11512200	Enhancers	A549	lung
32	chr2:11509800-11512400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:11509800-11512800	Weak transcription	Spleen	Spleen
34	chr2:11509800-11513800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:11509800-11514400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:11509800-11514400	Weak transcription	Fetal Brain Male	brain
37	chr2:11510600-11512000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:11510600-11512200	Enhancers	Hela-S3	cervix
39	chr2:11510600-11512400	Enhancers	NHEK	skin
40	chr2:11510600-11512600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr2:11510600-11512600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr2:11510600-11513800	Enhancers	Liver	Liver
43	chr2:11510600-11514200	Enhancers	NHDF-Ad	bronchial
44	chr2:11510600-11514600	Enhancers	HMEC	breast
45	chr2:11510600-11515000	Enhancers	Fetal Muscle Trunk	muscle
46	chr2:11510800-11512600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:11510800-11513600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:11510800-11514600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:11510800-11514600	Enhancers	Fetal Muscle Leg	muscle
50	chr2:11511000-11512000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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