Variant report

Variant	rs4670680
Chromosome Location	chr2:33770267-33770268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13388394	0.91[GIH][hapmap]
rs13388446	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13388566	0.93[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13406103	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13408890	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13415927	0.91[GIH][hapmap]
rs13425000	0.80[AMR][1000 genomes]
rs13426291	0.81[EUR][1000 genomes]
rs13428482	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1551486	0.86[GIH][hapmap];0.85[MEX][hapmap]
rs17597647	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17597696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1971224	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35933402	0.84[AMR][1000 genomes]
rs3845781	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs4670189	0.93[AMR][1000 genomes]
rs4670190	0.84[AMR][1000 genomes]
rs4670681	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670717	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6735997	0.82[GIH][hapmap]
rs7559049	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7605981	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828986	chr2:33758456-33772525	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
2	nsv516338	chr2:33758456-33780231	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	esv1805241	chr2:33759166-33772478	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	esv1846592	chr2:33761727-33772478	ZNF genes & repeats Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	esv1801323	chr2:33762787-33772478	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
6	esv1845579	chr2:33762787-33772478	Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	esv1809730	chr2:33764571-33770621	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv1849967	chr2:33764571-33770621	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
9	esv1817706	chr2:33764571-33772478	Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
10	esv1821368	chr2:33764571-33772478	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	esv1827397	chr2:33765311-33772525	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4670680	PRKD3	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33710400-33775400	Weak transcription	Pancreas	Pancrea
2	chr2:33738600-33782800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:33738800-33777200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:33740800-33790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:33747800-33780200	Weak transcription	Brain Anterior Caudate	brain
6	chr2:33748000-33774400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:33748000-33790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:33748200-33780200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:33755000-33779800	Weak transcription	Small Intestine	intestine
10	chr2:33755400-33779800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:33757000-33780000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:33757200-33809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:33760800-33782200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:33760800-33783600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:33761000-33789000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:33761200-33771000	Weak transcription	Right Ventricle	heart
17	chr2:33761200-33774200	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:33761200-33783800	Weak transcription	Psoas Muscle	Psoas
19	chr2:33762000-33780200	Weak transcription	Ovary	ovary
20	chr2:33762200-33772200	Weak transcription	Left Ventricle	heart
21	chr2:33762200-33775800	Weak transcription	Lung	lung
22	chr2:33762200-33777800	Weak transcription	Adipose Nuclei	Adipose
23	chr2:33762200-33779400	Weak transcription	Spleen	Spleen
24	chr2:33762200-33779600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:33762200-33809800	Weak transcription	Aorta	Aorta
26	chr2:33762600-33774200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:33763200-33780200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:33764800-33771600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:33765600-33775400	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:33765600-33784400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:33765800-33777800	Weak transcription	NHDF-Ad	bronchial
32	chr2:33766600-33771600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:33766800-33772600	Weak transcription	Fetal Heart	heart
34	chr2:33766800-33809800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:33767600-33779200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:33768200-33770600	Strong transcription	GM12878-XiMat	blood
37	chr2:33768800-33772600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:33769000-33770400	Weak transcription	Primary B cells from cord blood	blood

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