Variant report

Variant	rs12301714
Chromosome Location	chr12:51459277-51459278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51459276..51461108-chr12:51467854..51469536,2	MCF-7	breast:
2	chr12:51459011..51461192-chr12:51463959..51465473,2	K562	blood:
3	chr12:51450731..51453622-chr12:51457605..51459306,2	K562	blood:
4	chr12:51454870..51461450-chr12:51474103..51478804,12	K562	blood:
5	chr12:51455333..51457534-chr12:51459088..51463413,4	MCF-7	breast:
6	chr12:51455730..51461450-chr12:51475774..51478669,9	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11169693	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11542510	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11832566	0.94[YRI][hapmap]
rs12316220	1.00[YRI][hapmap]
rs12321533	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17125155	1.00[CEU][hapmap]
rs4238109	0.84[EUR][1000 genomes]
rs7342309	0.81[YRI][hapmap]
rs7966091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12301714	PRKAR1A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:51443600-51459600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:51443600-51462800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:51443800-51462600	Strong transcription	A549	lung
6	chr12:51444200-51463200	Strong transcription	Placenta	Placenta
7	chr12:51444200-51465000	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:51444200-51465400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:51444200-51465600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:51444200-51470400	Strong transcription	Fetal Stomach	stomach
11	chr12:51444400-51462800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr12:51444400-51464800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr12:51445000-51467800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:51445400-51462600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr12:51445400-51462600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:51445400-51462600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:51445400-51462800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:51445400-51464000	Strong transcription	Fetal Intestine Large	intestine
19	chr12:51445400-51467800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:51445400-51467800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr12:51445400-51469200	Strong transcription	Fetal Thymus	thymus
22	chr12:51445400-51470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:51445600-51462400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:51445600-51462800	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr12:51445600-51462800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:51445600-51462800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:51445600-51462800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr12:51445600-51462800	Strong transcription	Primary T cells from cord blood	blood
29	chr12:51445600-51463000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:51445600-51463000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:51445600-51463800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:51445600-51465200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr12:51445600-51467400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:51445600-51467800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:51445600-51467800	Strong transcription	Adipose Nuclei	Adipose
36	chr12:51445600-51468000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr12:51445600-51468400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:51445600-51469200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:51445600-51469800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:51445600-51470400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:51445600-51470600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:51445800-51462600	Strong transcription	Brain Anterior Caudate	brain
43	chr12:51445800-51462800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:51445800-51468000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:51445800-51468400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:51446000-51462800	Strong transcription	Dnd41	blood
47	chr12:51446000-51468400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:51446600-51463800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:51446800-51468600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:51447000-51462400	Strong transcription	Spleen	Spleen

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