Variant report

Variant	rs4398251
Chromosome Location	chr2:37554789-37554790
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:37554202-37555177	SK-N-SH	brain:	n/a	chr2:37554961-37554970 chr2:37554275-37554292 chr2:37554279-37554300 chr2:37554286-37554297
2	GATA3	chr2:37554458-37554992	SH-SY5Y	brain:	n/a	chr2:37554961-37554970
3	EP300	chr2:37554661-37555047	SK-N-SH_RA	brain:	n/a	n/a
4	GATA3	chr2:37553360-37555034	SK-N-SH	brain:	n/a	chr2:37554961-37554970 chr2:37554275-37554292 chr2:37554279-37554300 chr2:37554286-37554297
5	GATA2	chr2:37554265-37554994	SH-SY5Y	brain:	n/a	chr2:37554961-37554970 chr2:37554275-37554292 chr2:37554279-37554300 chr2:37554286-37554297
6	TCF12	chr2:37554166-37554982	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:37554747-37554797	NT2-D1	testis:	n/a
2	chr2:37554747-37554797	MCF-7	breast:	n/a
3	chr2:37554747-37554797	K562	blood:	n/a
4	chr2:37554747-37554797	SAEC	small airway:	n/a
5	chr2:37554747-37554797	SK-N-SH_RA	brain:	n/a
6	chr2:37554747-37554797	LNCaP	prostate:	n/a
7	chr2:37554747-37554797	HNPCEpiC	eye:	n/a
8	chr2:37554747-37554797	GM19239	blood:	n/a
9	chr2:37554747-37554797	ovcar-3	ovarian:	n/a
10	chr2:37554747-37554797	HCT-116	colon:	n/a
11	chr2:37554747-37554797	ECC-1	luminal epithelium:	n/a
12	chr2:37554747-37554797	HCF	heart:	n/a
13	chr2:37554747-37554797	GM06990	blood:	n/a
14	chr2:37554747-37554797	HAEpiC	amniotic membrane:	n/a
15	chr2:37554747-37554797	NHBE	bronchial:	n/a
16	chr2:37554747-37554797	GM12891	blood:	n/a
17	chr2:37554747-37554797	HCPEpiC	choroid plexus:	n/a
18	chr2:37554747-37554797	HEEpiC	esophagus:	n/a
19	chr2:37554747-37554797	BE2_C	brain:	n/a
20	chr2:37554747-37554797	HCM	heart:	n/a
21	chr2:37554747-37554797	PFSK-1	brain:	n/a
22	chr2:37554747-37554797	HepG2	liver:	n/a
23	chr2:37554747-37554797	T-47D	breast:	n/a
24	chr2:37554747-37554797	CMK	blood:	n/a
25	chr2:37554747-37554797	AG04450	lung:	fetal
26	chr2:37554747-37554797	NH-A	brain:	n/a
27	chr2:37554747-37554797	IMR90	lung:	fetal
28	chr2:37554747-37554797	ProgFib	skin:	n/a
29	chr2:37554747-37554797	SKMC	muscle:	n/a
30	chr2:37554747-37554797	PANC-1	pancreas:	n/a
31	chr2:37554747-37554797	HRPEpiC	eye:	n/a
32	chr2:37554747-37554797	RPTEC	kidney:	n/a
33	chr2:37554747-37554797	U87	brain:	n/a
34	chr2:37554747-37554797	BJ	skin:	n/a
35	chr2:37554747-37554797	AG09309	skin:	n/a
36	chr2:37554747-37554797	Hela-S3	cervix:	n/a
37	chr2:37554747-37554797	AG04449	skin:	fetal
38	chr2:37554747-37554797	HEK293	kidney:	embryo
39	chr2:37554747-37554797	GM12892	blood:	n/a
40	chr2:37554747-37554797	SK-N-MC	brain:	n/a
41	chr2:37554747-37554797	SK-N-SH	brain:	n/a
42	chr2:37554747-37554797	HUVEC	blood vessel:	n/a
43	chr2:37554747-37554797	HPAEpiC	pulmonary alveolar:	n/a
44	chr2:37554747-37554797	HRE	kidney:	n/a
45	chr2:37554747-37554797	MCF10A-Er-Src	breast:	n/a
46	chr2:37554747-37554797	AoSMC	blood vessel:	n/a
47	chr2:37554747-37554797	GM12878	blood:	n/a
48	chr2:37554747-37554797	AG10803	skin:	n/a
49	chr2:37554747-37554797	A549	lung:	n/a
50	chr2:37554747-37554797	PrEC	prostate:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:37545726..37548175-chr2:37554305..37557162,2	K562	blood:
2	chr2:37543073..37544935-chr2:37554432..37557348,2	K562	blood:
3	chr2:37553880..37556117-chr2:37565295..37568146,2	K562	blood:

No data

Variant related genes	Relation type
PRKD3	TF binding region
PRKD3	CpG island
ENSG00000115825	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10170761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017159	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174658	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10197287	1.00[ASN][1000 genomes]
rs10197856	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124571	1.00[ASN][1000 genomes]
rs11124572	1.00[ASN][1000 genomes]
rs11883585	1.00[ASN][1000 genomes]
rs11886853	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890709	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890754	1.00[ASN][1000 genomes]
rs11896614	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897904	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899003	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902292	1.00[ASN][1000 genomes]
rs13384958	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392784	1.00[ASN][1000 genomes]
rs13399143	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401288	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401291	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404663	0.80[AFR][1000 genomes]
rs13409402	1.00[ASN][1000 genomes]
rs13414561	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13422798	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424642	1.00[ASN][1000 genomes]
rs13426217	1.00[ASN][1000 genomes]
rs13426239	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426346	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426780	1.00[ASN][1000 genomes]
rs13429945	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17410072	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110966	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110967	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192945	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655786	1.00[ASN][1000 genomes]
rs28698067	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28710795	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34149238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59712801	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62133321	1.00[ASN][1000 genomes]
rs62133324	1.00[ASN][1000 genomes]
rs6711685	1.00[ASN][1000 genomes]
rs6715050	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726768	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726921	1.00[ASN][1000 genomes]
rs6727087	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727253	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730342	1.00[ASN][1000 genomes]
rs6733861	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748019	1.00[ASN][1000 genomes]
rs6749793	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750015	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752475	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754376	1.00[ASN][1000 genomes]
rs6754750	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755577	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761515	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72792882	1.00[ASN][1000 genomes]
rs7556904	1.00[ASN][1000 genomes]
rs7556959	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558593	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559558	1.00[ASN][1000 genomes]
rs7573871	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7582067	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590736	1.00[ASN][1000 genomes]
rs759460	1.00[ASN][1000 genomes]
rs7598671	1.00[ASN][1000 genomes]
rs888098	1.00[ASN][1000 genomes]
rs888099	1.00[ASN][1000 genomes]
rs9309005	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309006	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv2685	chr2:37550096-37594923	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4398251	PRKD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37553000-37555200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr2:37553200-37555000	Weak transcription	Small Intestine	intestine
3	chr2:37553800-37562200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:37554000-37557800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:37554200-37554800	Enhancers	Hela-S3	cervix
6	chr2:37554400-37554800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:37554400-37554800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:37554400-37554800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:37554400-37554800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:37554400-37555000	Enhancers	NHDF-Ad	bronchial
11	chr2:37554600-37554800	Active TSS	Adipose Nuclei	Adipose

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