Variant report

Variant	rs2016615
Chromosome Location	chr2:179347902-179347903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179347333..179349438-chr2:179354619..179356582,3	MCF-7	breast:
2	chr2:179315567..179317149-chr2:179346726..179348931,2	K562	blood:

Variant related genes	Relation type
ENSG00000180228	Chromatin interaction
ENSG00000204311	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10930831	0.84[ASN][1000 genomes]
rs12052983	0.96[ASN][1000 genomes]
rs1559908	0.80[ASN][1000 genomes]
rs16866342	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863671	0.80[ASN][1000 genomes]
rs1978580	0.98[ASN][1000 genomes]
rs2288322	0.89[ASN][1000 genomes]
rs2303537	0.92[ASN][1000 genomes]
rs2886712	0.87[ASN][1000 genomes]
rs33998881	0.83[ASN][1000 genomes]
rs3731754	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752689	0.87[ASN][1000 genomes]
rs3769866	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488846	0.83[ASN][1000 genomes]
rs6704545	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710856	0.91[ASN][1000 genomes]
rs6723399	0.84[ASN][1000 genomes]
rs6726043	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6735077	0.81[ASN][1000 genomes]
rs6739142	0.81[ASN][1000 genomes]
rs6753709	0.91[ASN][1000 genomes]
rs6758838	0.90[ASN][1000 genomes]
rs7575643	0.80[ASN][1000 genomes]
rs7587593	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7588593	0.83[ASN][1000 genomes]
rs7598228	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7600176	0.91[ASN][1000 genomes]
rs7602597	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs957875	0.81[ASN][1000 genomes]
rs967507	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9967820	0.83[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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2016615	PRKRA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346000-179348200	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr2:179346000-179348200	Enhancers	Spleen	Spleen
3	chr2:179346000-179350200	Enhancers	Small Intestine	intestine
4	chr2:179346000-179355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:179346200-179350000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:179346400-179348200	Enhancers	Pancreas	Pancrea
7	chr2:179346400-179349000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:179346400-179349400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:179346400-179349400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr2:179346400-179355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:179346400-179358600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:179346600-179348000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:179346600-179348000	Enhancers	Fetal Intestine Large	intestine
15	chr2:179346600-179348000	Enhancers	Fetal Intestine Small	intestine
16	chr2:179346600-179348000	Enhancers	Fetal Muscle Leg	muscle
17	chr2:179346600-179348400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:179346600-179349600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:179346600-179350200	Enhancers	Stomach Mucosa	stomach
20	chr2:179346600-179350400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:179346600-179351000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:179346600-179356200	Weak transcription	Colonic Mucosa	Colon
23	chr2:179346600-179358600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:179346800-179348000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:179346800-179348000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:179346800-179348000	Enhancers	Thymus	Thymus
27	chr2:179346800-179348400	Enhancers	Brain Cingulate Gyrus	brain
28	chr2:179346800-179349400	Enhancers	Brain Anterior Caudate	brain
29	chr2:179346800-179349800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:179346800-179349800	Enhancers	K562	blood
31	chr2:179346800-179350200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:179346800-179350200	Enhancers	Liver	Liver
33	chr2:179346800-179350200	Enhancers	Brain Substantia Nigra	brain
34	chr2:179346800-179350200	Enhancers	Right Ventricle	heart
35	chr2:179346800-179350400	Enhancers	Colon Smooth Muscle	Colon
36	chr2:179347000-179348000	Enhancers	Esophagus	oesophagus
37	chr2:179347000-179350800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:179347200-179348000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr2:179347200-179348000	Enhancers	Aorta	Aorta
40	chr2:179347200-179348000	Enhancers	Fetal Brain Male	brain
41	chr2:179347200-179348200	Enhancers	Brain Angular Gyrus	brain
42	chr2:179347200-179348200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:179347200-179348400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:179347200-179348400	Weak transcription	Osteobl	bone
45	chr2:179347200-179349400	Weak transcription	NHLF	lung
46	chr2:179347200-179349600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:179347200-179349600	Enhancers	HepG2	liver
48	chr2:179347200-179349800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:179347200-179349800	Enhancers	Left Ventricle	heart
50	chr2:179347200-179350200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links