Variant report

Variant	rs2366604
Chromosome Location	chr2:179292766-179292767
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:179292206..179295495-chr2:179302898..179306036,3	K562	blood:
2	chr2:179292126..179294038-chr2:179308738..179311324,2	K562	blood:
3	chr2:179283998..179286629-chr2:179290509..179293142,4	K562	blood:
4	chr2:179286570..179288452-chr2:179289828..179294191,4	K562	blood:
5	chr2:179290672..179296705-chr2:179311873..179319969,11	K562	blood:
6	chr2:179290293..179297501-chr2:179307356..179318778,14	K562	blood:
7	chr2:179291608..179296531-chr2:179313533..179317372,6	MCF-7	breast:
8	chr2:179290477..179293762-chr2:179342502..179345312,3	MCF-7	breast:
9	chr2:179289040..179292034-chr2:179292711..179296035,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180228	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000079150	Chromatin interaction
ENSG00000238082	Chromatin interaction
ENSG00000204311	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10179153	0.96[ASN][1000 genomes]
rs10207436	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930831	0.84[ASN][1000 genomes]
rs13411588	0.95[ASN][1000 genomes]
rs2114582	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2366603	0.95[ASN][1000 genomes]
rs2886712	0.83[ASN][1000 genomes]
rs3752689	0.83[ASN][1000 genomes]
rs4894017	0.93[ASN][1000 genomes]
rs4894018	0.95[ASN][1000 genomes]
rs4894019	0.95[ASN][1000 genomes]
rs4894020	0.95[ASN][1000 genomes]
rs6739142	0.89[ASN][1000 genomes]
rs7589679	0.93[ASN][1000 genomes]
rs9288019	0.93[ASN][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	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
2	nsv979349	chr2:179279539-179296355	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2366604	PRKRA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179278800-179292800	Weak transcription	Spleen	Spleen
2	chr2:179278800-179293200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:179278800-179298800	Weak transcription	Small Intestine	intestine
4	chr2:179279600-179295000	Weak transcription	Right Ventricle	heart
5	chr2:179279600-179298800	Weak transcription	Colonic Mucosa	Colon
6	chr2:179279800-179293800	Weak transcription	Placenta	Placenta
7	chr2:179279800-179295400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:179279800-179299200	Weak transcription	Esophagus	oesophagus
9	chr2:179279800-179313800	Weak transcription	Stomach Mucosa	stomach
10	chr2:179280000-179293600	Weak transcription	Liver	Liver
11	chr2:179280000-179293800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:179280000-179294000	Weak transcription	Brain Substantia Nigra	brain
13	chr2:179280000-179296800	Weak transcription	NHLF	lung
14	chr2:179280000-179297600	Weak transcription	Hela-S3	cervix
15	chr2:179280000-179298400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:179280000-179305200	Weak transcription	Fetal Brain Male	brain
17	chr2:179280000-179310600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:179280200-179293800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:179280200-179293800	Weak transcription	HUVEC	blood vessel
20	chr2:179280200-179296600	Weak transcription	Fetal Kidney	kidney
21	chr2:179280200-179314600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:179280400-179294000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:179280800-179294000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:179283400-179294400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:179284400-179295400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:179285800-179294200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:179286800-179293800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:179287600-179294000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:179287600-179295200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:179289800-179293000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:179290200-179312800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:179290400-179294800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:179290400-179296600	Weak transcription	Psoas Muscle	Psoas
34	chr2:179290600-179296400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:179290800-179293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:179290800-179312000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:179290800-179312600	Strong transcription	Dnd41	blood
38	chr2:179291000-179292800	Weak transcription	Fetal Intestine Large	intestine
39	chr2:179291000-179293200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:179291000-179300600	Strong transcription	Thymus	Thymus
41	chr2:179291000-179300800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:179291000-179311600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:179291000-179313200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:179291000-179313400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:179291000-179313600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:179291200-179292800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:179291200-179292800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:179291200-179294600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:179291200-179296400	Strong transcription	Fetal Stomach	stomach
50	chr2:179291200-179298400	Weak transcription	Fetal Intestine Small	intestine

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