Variant report

Variant	rs6758838
Chromosome Location	chr2:179321904-179321905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179313693..179317837-chr2:179319182..179322709,8	K562	blood:
2	chr17:48795662..48798133-chr2:179321396..179323365,2	MCF-7	breast:
3	chr2:179319205..179322423-chr2:179341743..179345832,4	K562	blood:
4	chr2:179314981..179317756-chr2:179318011..179323890,9	K562	blood:
5	chr2:179318690..179321554-chr2:179321792..179324327,3	K562	blood:
6	chr2:179320916..179326007-chr2:179328334..179330318,5	K562	blood:
7	chr2:179320916..179324628-chr2:179328091..179329967,4	K562	blood:

Variant related genes	Relation type
ENSG00000116095	Chromatin interaction
ENSG00000238082	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000079150	Chromatin interaction
ENSG00000108848	Chromatin interaction
ENSG00000180228	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10930831	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052983	0.86[ASN][1000 genomes]
rs13382684	0.80[EUR][1000 genomes]
rs13411588	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16866342	0.90[ASN][1000 genomes]
rs1967327	0.80[EUR][1000 genomes]
rs1978580	0.88[ASN][1000 genomes]
rs2016615	0.90[ASN][1000 genomes]
rs2288322	0.96[ASN][1000 genomes]
rs2303537	0.82[ASN][1000 genomes]
rs2366603	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2886712	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731754	0.88[ASN][1000 genomes]
rs3752689	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769866	0.90[ASN][1000 genomes]
rs4894018	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4894019	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4894020	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6704545	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6710856	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6726043	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739142	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6753709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587593	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7598228	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7600176	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7602597	0.87[ASN][1000 genomes]
rs967507	0.88[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
rs6758838	PRKRA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179316800-179322000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:179316800-179327800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:179316800-179329000	Weak transcription	Liver	Liver
4	chr2:179316800-179329400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:179316800-179329800	Weak transcription	Ovary	ovary
6	chr2:179316800-179338200	Weak transcription	Fetal Stomach	stomach
7	chr2:179316800-179338800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:179316800-179341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:179316800-179342400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:179316800-179342600	Weak transcription	Aorta	Aorta
11	chr2:179316800-179342800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:179317000-179329000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:179317000-179342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:179317200-179328800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:179317200-179329200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:179317200-179329200	Weak transcription	Dnd41	blood
17	chr2:179317200-179342800	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:179317400-179341200	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:179317400-179341600	Weak transcription	GM12878-XiMat	blood
20	chr2:179317800-179329200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:179317800-179329200	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:179317800-179338200	Weak transcription	Osteobl	bone
23	chr2:179318000-179322600	Weak transcription	Fetal Lung	lung
24	chr2:179318000-179329200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:179318000-179332400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:179318000-179334200	Weak transcription	Fetal Kidney	kidney
27	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:179319400-179323000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:179320200-179329200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:179320800-179329400	Weak transcription	NH-A	brain
31	chr2:179321000-179329000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:179321200-179329400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:179321200-179342400	Weak transcription	HSMM	muscle
34	chr2:179321200-179342400	Weak transcription	HSMMtube	muscle
35	chr2:179321600-179323600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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