Variant report

Variant	rs56309550
Chromosome Location	chr6:34282123-34282124
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10484267	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484268	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057691	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883896	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888452	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628798	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17628946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629180	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629270	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696583	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696774	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696829	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1994923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs206922	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798554	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798557	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269032	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41269034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269038	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55684754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55694290	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55763242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798596	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55812200	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833185	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55863933	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864834	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56033036	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56039915	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56107559	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188036	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56274913	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56323997	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56330729	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59832183	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes]
rs6911272	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7741127	0.80[AMR][1000 genomes]
rs7760373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770443	0.84[EUR][1000 genomes]
rs875274	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9368811	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv1794528	chr6:34267024-34308816	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56309550	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:34262000-34282600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr6:34262000-34282800	Weak transcription	Primary T cells from cord blood	blood
5	chr6:34262000-34283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:34262000-34284600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:34262000-34286600	Weak transcription	Gastric	stomach
8	chr6:34262000-34289000	Weak transcription	Hela-S3	cervix
9	chr6:34262000-34292800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:34262200-34295400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:34262200-34301200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:34262800-34290800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:34263800-34282800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:34263800-34288400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:34264000-34282400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:34264000-34299000	Weak transcription	Dnd41	blood
17	chr6:34264600-34282400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:34264600-34284400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:34267400-34283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:34268600-34283400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:34269400-34282200	Weak transcription	Fetal Thymus	thymus
22	chr6:34269400-34282400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:34269600-34286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:34269800-34284200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:34270000-34283600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:34272600-34288200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:34273600-34283000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:34274000-34283600	Weak transcription	Fetal Kidney	kidney
29	chr6:34274200-34285000	Weak transcription	Fetal Intestine Small	intestine
30	chr6:34274200-34285000	Weak transcription	HSMMtube	muscle
31	chr6:34274400-34282600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:34274400-34282600	Weak transcription	Brain Anterior Caudate	brain
33	chr6:34274400-34306400	Weak transcription	Brain Germinal Matrix	brain
34	chr6:34274400-34309000	Weak transcription	NHDF-Ad	bronchial
35	chr6:34274600-34283000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:34274800-34285200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:34275000-34284200	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:34275000-34285400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:34275200-34285800	Weak transcription	Fetal Stomach	stomach
40	chr6:34275200-34298000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:34275400-34284400	Weak transcription	Right Ventricle	heart
42	chr6:34275400-34285200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:34275400-34286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:34275400-34289400	Weak transcription	HUVEC	blood vessel
45	chr6:34275600-34283600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:34275800-34299600	Weak transcription	Lung	lung
47	chr6:34276200-34283800	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:34276200-34284400	Weak transcription	Right Atrium	heart
49	chr6:34276200-34286800	Weak transcription	Ovary	ovary
50	chr6:34276400-34287000	Weak transcription	HepG2	liver

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