Variant report

Variant	rs1863671
Chromosome Location	chr2:179342330-179342331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr2:179342070-179342697	HepG2	liver:	n/a	n/a
2	MXI1	chr2:179341626-179344256	SK-N-SH	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:76970332..76972740-chr2:179341961..179344883,2	MCF-7	breast:
2	chr2:179277322..179281063-chr2:179341771..179345640,5	K562	blood:
3	chr2:179312045..179317660-chr2:179337933..179347437,24	MCF-7	breast:
4	chr2:178976808..178978488-chr2:179342162..179344754,2	MCF-7	breast:
5	chr2:179319205..179322423-chr2:179341743..179345832,4	K562	blood:
6	chr2:179310863..179318324-chr2:179338966..179346608,29	K562	blood:
7	chr2:179341858..179343792-chr2:179500377..179502025,2	K562	blood:
8	chr2:179314444..179318442-chr2:179340876..179346721,19	MCF-7	breast:
9	chr2:179311363..179318324-chr2:179340414..179346232,28	K562	blood:
10	chr2:178127221..178129853-chr2:179341742..179345099,3	K562	blood:
11	chr2:179308416..179311292-chr2:179342166..179344945,2	MCF-7	breast:
12	chr2:179278151..179280958-chr2:179342121..179344961,4	K562	blood:

No data

Variant related genes	Relation type
PLEKHA3	TF binding region
ENSG00000155636	Chromatin interaction
ENSG00000180228	Chromatin interaction
ENSG00000222043	Chromatin interaction
ENSG00000223960	Chromatin interaction
ENSG00000238082	Chromatin interaction
ENSG00000237298	Chromatin interaction
ENSG00000116044	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000165637	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12615347	0.90[ASN][1000 genomes]
rs13382684	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1559908	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866334	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866342	0.80[ASN][1000 genomes]
rs1967327	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2016615	0.80[ASN][1000 genomes]
rs2288320	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2303536	0.82[ASN][1000 genomes]
rs33998881	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3769866	0.80[ASN][1000 genomes]
rs60488846	0.98[ASN][1000 genomes]
rs6704545	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726043	0.83[ASN][1000 genomes]
rs7575643	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587593	0.83[ASN][1000 genomes]
rs7588593	0.98[ASN][1000 genomes]
rs7598228	0.83[ASN][1000 genomes]
rs8179648	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9967820	0.82[AMR][1000 genomes];0.98[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
rs1863671	PRKRA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179316800-179342400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:179316800-179342600	Weak transcription	Aorta	Aorta
3	chr2:179316800-179342800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:179317200-179342800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:179318000-179342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:179321200-179342400	Weak transcription	HSMM	muscle
7	chr2:179321200-179342400	Weak transcription	HSMMtube	muscle
8	chr2:179326200-179342400	Weak transcription	Adipose Nuclei	Adipose
9	chr2:179326200-179342600	Weak transcription	Primary T cells from cord blood	blood
10	chr2:179327000-179342400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:179327200-179342400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:179328200-179342600	Weak transcription	Fetal Thymus	thymus
13	chr2:179328200-179342600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:179330600-179342400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:179330800-179342600	Weak transcription	Colonic Mucosa	Colon
16	chr2:179331200-179342800	Weak transcription	Lung	lung
17	chr2:179331600-179342400	Weak transcription	Psoas Muscle	Psoas
18	chr2:179332800-179342600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:179333000-179342400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:179334200-179342400	Weak transcription	Primary B cells from cord blood	blood
21	chr2:179334200-179342400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:179335000-179342400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:179339000-179342600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:179339000-179342600	Weak transcription	Right Ventricle	heart
25	chr2:179339200-179342400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:179339400-179342800	Weak transcription	Fetal Heart	heart
27	chr2:179339600-179342400	Weak transcription	Fetal Stomach	stomach
28	chr2:179339800-179342800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:179339800-179342800	Weak transcription	Left Ventricle	heart
30	chr2:179341000-179342400	Weak transcription	Fetal Brain Male	brain
31	chr2:179341200-179342800	Flanking Active TSS	Dnd41	blood
32	chr2:179341200-179346000	Active TSS	Fetal Brain Female	brain
33	chr2:179341400-179343600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:179341400-179344200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:179341600-179342400	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:179341600-179342600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:179341600-179344200	Active TSS	Fetal Lung	lung
38	chr2:179341800-179342400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:179341800-179342400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:179341800-179342400	Enhancers	Fetal Intestine Small	intestine
41	chr2:179341800-179342400	Enhancers	Osteobl	bone
42	chr2:179341800-179343200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:179341800-179343400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:179341800-179343600	Active TSS	NH-A	brain
45	chr2:179341800-179343600	Active TSS	NHLF	lung
46	chr2:179341800-179344000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:179341800-179344000	Active TSS	Ovary	ovary
48	chr2:179341800-179345000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:179341800-179345600	Active TSS	Brain Germinal Matrix	brain
50	chr2:179341800-179345800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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